diff --git a/crates/ruff/tests/format.rs b/crates/ruff/tests/format.rs
index 35443daa2394b..f1369048f7326 100644
--- a/crates/ruff/tests/format.rs
+++ b/crates/ruff/tests/format.rs
@@ -500,6 +500,35 @@ OTHER = "OTHER"
     Ok(())
 }
 
+/// Regression test for <https://github.com/astral-sh/ruff/issues/20035>
+#[test]
+fn deduplicate_directory_and_explicit_file() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let root = tempdir.path();
+
+    let main = root.join("main.py");
+    fs::write(&main, "x   = 1\n")?;
+
+    assert_cmd_snapshot!(
+        Command::new(get_cargo_bin(BIN_NAME))
+            .current_dir(root)
+            .args(["format", "--no-cache", "--check"])
+            .arg(".")
+            .arg("main.py"),
+        @r"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    Would reformat: main.py
+    1 file would be reformatted
+
+    ----- stderr -----
+    "
+    );
+
+    Ok(())
+}
+
 #[test]
 fn syntax_error() -> Result<()> {
     let tempdir = TempDir::new()?;
diff --git a/crates/ruff/tests/lint.rs b/crates/ruff/tests/lint.rs
index b54e69996d197..492665555a071 100644
--- a/crates/ruff/tests/lint.rs
+++ b/crates/ruff/tests/lint.rs
@@ -271,6 +271,50 @@ OTHER = "OTHER"
     Ok(())
 }
 
+/// Regression test for <https://github.com/astral-sh/ruff/issues/20035>
+#[test]
+fn deduplicate_directory_and_explicit_file() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let root = tempdir.path();
+    let ruff_toml = tempdir.path().join("ruff.toml");
+    fs::write(
+        &ruff_toml,
+        r#"
+[lint]
+exclude = ["main.py"]
+"#,
+    )?;
+
+    let main = root.join("main.py");
+    fs::write(&main, "import os\n")?;
+
+    insta::with_settings!({
+        filters => vec![(tempdir_filter(&tempdir).as_str(), "[TMP]/")]
+    }, {
+        assert_cmd_snapshot!(
+            Command::new(get_cargo_bin(BIN_NAME))
+                .current_dir(root)
+                .args(STDIN_BASE_OPTIONS)
+                .args(["--config", &ruff_toml.file_name().unwrap().to_string_lossy()])
+                .arg(".")
+                // Explicitly pass main.py, should be linted regardless of it being excluded by lint.exclude
+                .arg("main.py"),
+            @r"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    main.py:1:8: F401 [*] `os` imported but unused
+    Found 1 error.
+    [*] 1 fixable with the `--fix` option.
+
+    ----- stderr -----
+    "
+        );
+    });
+
+    Ok(())
+}
+
 #[test]
 fn exclude_stdin() -> Result<()> {
     let tempdir = TempDir::new()?;
diff --git a/crates/ruff_workspace/src/resolver.rs b/crates/ruff_workspace/src/resolver.rs
index 84a31ebbeea4f..d6e642ed486e5 100644
--- a/crates/ruff_workspace/src/resolver.rs
+++ b/crates/ruff_workspace/src/resolver.rs
@@ -523,10 +523,42 @@ impl<'config> WalkPythonFilesState<'config> {
         let (files, error) = self.merged.into_inner().unwrap();
         error?;
 
-        Ok((files, self.resolver.into_inner().unwrap()))
+        let deduplicated_files = deduplicate_files(files);
+
+        Ok((deduplicated_files, self.resolver.into_inner().unwrap()))
     }
 }
 
+/// Deduplicate files by path, prioritizing `Root` files over `Nested` files.
+///
+/// When the same path appears both as a directly specified input (`Root`)
+/// and via directory traversal (`Nested`), keep the `Root` entry and drop
+/// the `Nested` entry.
+///
+/// Dropping the root entry means that the explicitly passed path may be
+/// unintentionally ignored, since it is treated as nested and can be excluded
+/// despite being requested.
+///
+/// Concretely, with `lint.exclude = ["foo.py"]` and `ruff check . foo.py`,
+/// we must keep `Root(foo.py)` and drop `Nested(foo.py)` so `foo.py` is
+/// linted as the user requested.
+fn deduplicate_files(mut files: ResolvedFiles) -> ResolvedFiles {
+    // Sort by path; for identical paths, prefer Root over Nested; place errors after files
+    files.sort_by(|a, b| match (a, b) {
+        (Ok(a_file), Ok(b_file)) => a_file.cmp(b_file),
+        (Ok(_), Err(_)) => Ordering::Less,
+        (Err(_), Ok(_)) => Ordering::Greater,
+        (Err(_), Err(_)) => Ordering::Equal,
+    });
+
+    files.dedup_by(|a, b| match (a, b) {
+        (Ok(a_file), Ok(b_file)) => a_file.path() == b_file.path(),
+        _ => false,
+    });
+
+    files
+}
+
 struct PythonFilesVisitorBuilder<'s, 'config> {
     state: &'s WalkPythonFilesState<'config>,
     transformer: &'s (dyn ConfigurationTransformer + Sync),
@@ -682,7 +714,7 @@ impl Drop for PythonFilesVisitor<'_, '_> {
     }
 }
 
-#[derive(Clone, Debug, PartialEq, Eq)]
+#[derive(Clone, Debug, PartialEq, Eq, Ord, PartialOrd)]
 pub enum ResolvedFile {
     /// File explicitly passed to the CLI
     Root(PathBuf),
@@ -715,18 +747,6 @@ impl ResolvedFile {
     }
 }
 
-impl PartialOrd for ResolvedFile {
-    fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
-        Some(self.cmp(other))
-    }
-}
-
-impl Ord for ResolvedFile {
-    fn cmp(&self, other: &Self) -> Ordering {
-        self.path().cmp(other.path())
-    }
-}
-
 /// Return `true` if the Python file at [`Path`] is _not_ excluded.
 pub fn python_file_at_path(
     path: &Path,