diff --git a/esphome/__main__.py b/esphome/__main__.py
index 16fa32ee96..21c5db606e 100644
--- a/esphome/__main__.py
+++ b/esphome/__main__.py
@@ -259,13 +259,17 @@ def choose_upload_log_host(
     ]
 
     # Add RP2040 BOOTSEL device option when uploading
+    bootsel_permission_error = False
     if (
         purpose == Purpose.UPLOADING
         and CORE.data.get(KEY_CORE, {}).get(KEY_TARGET_PLATFORM) == PLATFORM_RP2040
         and (picotool := _find_picotool()) is not None
-        and detect_rp2040_bootsel(picotool) > 0
     ):
-        options.append(("RP2040 BOOTSEL (via picotool)", "BOOTSEL"))
+        bootsel = detect_rp2040_bootsel(picotool)
+        if bootsel.device_count > 0:
+            options.append(("RP2040 BOOTSEL (via picotool)", "BOOTSEL"))
+        elif bootsel.permission_error:
+            bootsel_permission_error = True
 
     if purpose == Purpose.LOGGING:
         if has_mqtt_logging():
@@ -290,6 +294,17 @@ def choose_upload_log_host(
         and CORE.data.get(KEY_CORE, {}).get(KEY_TARGET_PLATFORM) == PLATFORM_RP2040
         and not any(get_port_type(opt[1]) == PortType.BOOTSEL for opt in options)
     ):
+        if bootsel_permission_error:
+            _LOGGER.warning(
+                "An RP2040 device in BOOTSEL mode was detected but could "
+                "not be accessed due to USB permissions."
+            )
+            if sys.platform.startswith("linux"):
+                _LOGGER.warning(
+                    "You may need to add a udev rule for RP2040 devices. "
+                    "See: https://github.com/raspberrypi/picotool"
+                    "/blob/master/udev/60-picotool.rules"
+                )
         if not options:
             raise EsphomeError(
                 f"No RP2040 device found. {_RP2040_BOOTSEL_INSTRUCTIONS}"
@@ -824,7 +839,8 @@ def upload_using_picotool(config: ConfigType) -> int:
             if sys.platform.startswith("linux"):
                 msg += (
                     " You may need to add udev rules for RP2040 devices."
-                    " See: https://github.com/raspberrypi/picotool#linux-permissions"
+                    " See: https://github.com/raspberrypi/picotool"
+                    "/blob/master/udev/60-picotool.rules"
                 )
             _LOGGER.error(msg)
         else:
diff --git a/esphome/util.py b/esphome/util.py
index d0fa4300a9..7c4166c48b 100644
--- a/esphome/util.py
+++ b/esphome/util.py
@@ -1,5 +1,6 @@
 import collections
 from collections.abc import Callable
+from dataclasses import dataclass
 import io
 import logging
 from pathlib import Path
@@ -376,11 +377,19 @@ def get_picotool_path(cc_path: str) -> Path | None:
     return None
 
 
-def detect_rp2040_bootsel(picotool_path: str | Path) -> int:
+@dataclass
+class BootselResult:
+    """Result of RP2040 BOOTSEL detection."""
+
+    device_count: int
+    permission_error: bool = False
+
+
+def detect_rp2040_bootsel(picotool_path: str | Path) -> BootselResult:
     """Detect RP2040/RP2350 devices in BOOTSEL mode using picotool.
 
-    Returns the number of devices found (by counting 'type:' lines in output),
-    matching PlatformIO's detection approach.
+    Returns a BootselResult with the number of devices found (by counting
+    'type:' lines in output), and whether a permission error was detected.
     """
     try:
         result = subprocess.run(
@@ -389,9 +398,17 @@ def detect_rp2040_bootsel(picotool_path: str | Path) -> int:
             timeout=10,
             check=False,
         )
-        return result.stdout.count(b"type:")
+        device_count = result.stdout.count(b"type:")
+        if device_count > 0:
+            return BootselResult(device_count)
+        # Check stderr for permission issues — picotool can see the device
+        # on the USB bus but can't connect without proper permissions
+        combined = result.stderr + result.stdout
+        if b"unable to connect" in combined or b"LIBUSB_ERROR_ACCESS" in combined:
+            return BootselResult(0, permission_error=True)
+        return BootselResult(0)
     except (OSError, subprocess.TimeoutExpired):
-        return 0
+        return BootselResult(0)
 
 
 def get_esp32_arduino_flash_error_help() -> str | None:
diff --git a/tests/unit_tests/test_main.py b/tests/unit_tests/test_main.py
index 817a18e2b9..b6f1a28086 100644
--- a/tests/unit_tests/test_main.py
+++ b/tests/unit_tests/test_main.py
@@ -73,6 +73,7 @@ from esphome.const import (
     PLATFORM_RP2040,
 )
 from esphome.core import CORE, EsphomeError
+from esphome.util import BootselResult
 
 
 def strip_ansi_codes(text: str) -> str:
@@ -872,7 +873,7 @@ def test_choose_upload_log_host_no_defaults_with_rp2040_bootsel(
         patch(
             "esphome.__main__._find_picotool", return_value=Path("/usr/bin/picotool")
         ),
-        patch("esphome.__main__.detect_rp2040_bootsel", return_value=1),
+        patch("esphome.__main__.detect_rp2040_bootsel", return_value=BootselResult(1)),
     ):
         result = choose_upload_log_host(
             default=None,
@@ -895,7 +896,7 @@ def test_choose_upload_log_host_rp2040_no_device_shows_bootsel_help() -> None:
         patch(
             "esphome.__main__._find_picotool", return_value=Path("/usr/bin/picotool")
         ),
-        patch("esphome.__main__.detect_rp2040_bootsel", return_value=0),
+        patch("esphome.__main__.detect_rp2040_bootsel", return_value=BootselResult(0)),
         pytest.raises(EsphomeError, match="BOOTSEL"),
     ):
         choose_upload_log_host(
@@ -920,7 +921,7 @@ def test_choose_upload_log_host_rp2040_bootsel_tip_with_ota(
         patch(
             "esphome.__main__._find_picotool", return_value=Path("/usr/bin/picotool")
         ),
-        patch("esphome.__main__.detect_rp2040_bootsel", return_value=0),
+        patch("esphome.__main__.detect_rp2040_bootsel", return_value=BootselResult(0)),
         patch(
             "esphome.__main__.choose_prompt",
             return_value="192.168.1.100",
@@ -949,7 +950,7 @@ def test_choose_upload_log_host_rp2040_bootsel_tip_with_serial_ports(
             "esphome.__main__._find_picotool",
             return_value=Path("/usr/bin/picotool"),
         ),
-        patch("esphome.__main__.detect_rp2040_bootsel", return_value=0),
+        patch("esphome.__main__.detect_rp2040_bootsel", return_value=BootselResult(0)),
         caplog.at_level(logging.INFO, logger="esphome.__main__"),
     ):
         choose_upload_log_host(
@@ -960,6 +961,69 @@ def test_choose_upload_log_host_rp2040_bootsel_tip_with_serial_ports(
         assert "BOOTSEL" in caplog.text
 
 
+@pytest.mark.usefixtures("mock_no_serial_ports")
+def test_choose_upload_log_host_rp2040_permission_error_no_options(
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """Test permission warning shown when BOOTSEL device found but not accessible."""
+    setup_core(platform=PLATFORM_RP2040)
+
+    with (
+        patch(
+            "esphome.__main__._find_picotool", return_value=Path("/usr/bin/picotool")
+        ),
+        patch(
+            "esphome.__main__.detect_rp2040_bootsel",
+            return_value=BootselResult(0, permission_error=True),
+        ),
+        patch("esphome.__main__.sys.platform", "linux"),
+        pytest.raises(EsphomeError, match="BOOTSEL"),
+        caplog.at_level(logging.WARNING, logger="esphome.__main__"),
+    ):
+        choose_upload_log_host(
+            default=None,
+            check_default=None,
+            purpose=Purpose.UPLOADING,
+        )
+
+    assert "USB permissions" in caplog.text
+    assert "udev" in caplog.text
+
+
+@pytest.mark.usefixtures("mock_no_serial_ports")
+def test_choose_upload_log_host_rp2040_permission_error_with_ota(
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """Test permission warning shown with OTA fallback available."""
+    setup_core(
+        platform=PLATFORM_RP2040,
+        config={CONF_OTA: [{CONF_PLATFORM: CONF_ESPHOME}]},
+        address="192.168.1.100",
+    )
+
+    with (
+        patch(
+            "esphome.__main__._find_picotool", return_value=Path("/usr/bin/picotool")
+        ),
+        patch(
+            "esphome.__main__.detect_rp2040_bootsel",
+            return_value=BootselResult(0, permission_error=True),
+        ),
+        patch(
+            "esphome.__main__.choose_prompt",
+            return_value="192.168.1.100",
+        ),
+        caplog.at_level(logging.WARNING, logger="esphome.__main__"),
+    ):
+        choose_upload_log_host(
+            default=None,
+            check_default=None,
+            purpose=Purpose.UPLOADING,
+        )
+
+    assert "USB permissions" in caplog.text
+
+
 def test_choose_upload_log_host_no_bootsel_for_non_rp2040(
     mock_no_serial_ports: Mock,
 ) -> None:
@@ -997,7 +1061,7 @@ def test_choose_upload_log_host_rp2040_serial_and_bootsel(
         patch(
             "esphome.__main__._find_picotool", return_value=Path("/usr/bin/picotool")
         ),
-        patch("esphome.__main__.detect_rp2040_bootsel", return_value=1),
+        patch("esphome.__main__.detect_rp2040_bootsel", return_value=BootselResult(1)),
     ):
         choose_upload_log_host(
             default=None,
diff --git a/tests/unit_tests/test_util.py b/tests/unit_tests/test_util.py
index 73fd6b34e2..ca3fd9b78a 100644
--- a/tests/unit_tests/test_util.py
+++ b/tests/unit_tests/test_util.py
@@ -461,8 +461,9 @@ def test_detect_rp2040_bootsel_found() -> None:
     mock_result = MagicMock()
     mock_result.stdout = b"Device Information\n type: RP2040\n"
     with patch("esphome.util.subprocess.run", return_value=mock_result):
-        count = util.detect_rp2040_bootsel("/usr/bin/picotool")
-    assert count == 1
+        result = util.detect_rp2040_bootsel("/usr/bin/picotool")
+    assert result.device_count == 1
+    assert result.permission_error is False
 
 
 def test_detect_rp2040_bootsel_multiple() -> None:
@@ -470,8 +471,9 @@ def test_detect_rp2040_bootsel_multiple() -> None:
     mock_result = MagicMock()
     mock_result.stdout = b"type: RP2040\ntype: RP2350\n"
     with patch("esphome.util.subprocess.run", return_value=mock_result):
-        count = util.detect_rp2040_bootsel("/usr/bin/picotool")
-    assert count == 2
+        result = util.detect_rp2040_bootsel("/usr/bin/picotool")
+    assert result.device_count == 2
+    assert result.permission_error is False
 
 
 def test_detect_rp2040_bootsel_none() -> None:
@@ -480,16 +482,47 @@ def test_detect_rp2040_bootsel_none() -> None:
     mock_result.stdout = (
         b"No accessible RP2040/RP2350 devices in BOOTSEL mode were found.\n"
     )
+    mock_result.stderr = b""
     with patch("esphome.util.subprocess.run", return_value=mock_result):
-        count = util.detect_rp2040_bootsel("/usr/bin/picotool")
-    assert count == 0
+        result = util.detect_rp2040_bootsel("/usr/bin/picotool")
+    assert result.device_count == 0
+    assert result.permission_error is False
+
+
+def test_detect_rp2040_bootsel_permission_error() -> None:
+    """Test BOOTSEL detection with device found but not accessible."""
+    mock_result = MagicMock()
+    mock_result.stdout = (
+        b"No accessible RP-series devices in BOOTSEL mode were found.\n"
+    )
+    mock_result.stderr = (
+        b"RP2040 device at bus 5, address 24 appears to be in BOOTSEL mode, "
+        b"but picotool was unable to connect. "
+        b"Maybe try 'sudo' or check your permissions.\n"
+    )
+    with patch("esphome.util.subprocess.run", return_value=mock_result):
+        result = util.detect_rp2040_bootsel("/usr/bin/picotool")
+    assert result.device_count == 0
+    assert result.permission_error is True
+
+
+def test_detect_rp2040_bootsel_libusb_access_error() -> None:
+    """Test BOOTSEL detection with LIBUSB_ERROR_ACCESS."""
+    mock_result = MagicMock()
+    mock_result.stdout = b""
+    mock_result.stderr = b"LIBUSB_ERROR_ACCESS\n"
+    with patch("esphome.util.subprocess.run", return_value=mock_result):
+        result = util.detect_rp2040_bootsel("/usr/bin/picotool")
+    assert result.device_count == 0
+    assert result.permission_error is True
 
 
 def test_detect_rp2040_bootsel_oserror() -> None:
     """Test BOOTSEL detection handles OSError."""
     with patch("esphome.util.subprocess.run", side_effect=OSError("not found")):
-        count = util.detect_rp2040_bootsel("/usr/bin/picotool")
-    assert count == 0
+        result = util.detect_rp2040_bootsel("/usr/bin/picotool")
+    assert result.device_count == 0
+    assert result.permission_error is False
 
 
 def test_detect_rp2040_bootsel_timeout() -> None:
@@ -498,5 +531,6 @@ def test_detect_rp2040_bootsel_timeout() -> None:
         "esphome.util.subprocess.run",
         side_effect=subprocess.TimeoutExpired("picotool", 10),
     ):
-        count = util.detect_rp2040_bootsel("/usr/bin/picotool")
-    assert count == 0
+        result = util.detect_rp2040_bootsel("/usr/bin/picotool")
+    assert result.device_count == 0
+    assert result.permission_error is False