diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f0505ed60..6dbd5817a7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -106,6 +106,8 @@ END_UNRELEASED_TEMPLATE
 * (toolchains) use "command -v" to find interpreter in `$PATH`
   ([#3150](https://github.com/bazel-contrib/rules_python/pull/3150)).
 * (pypi) `bazel vendor` now works in `bzlmod` ({gh-issue}`3079`).
+* (gazelle) Remove py_binary targets with invalid srcs. This includes files
+  that are not generated or regular files.
 
 {#v0-0-0-added}
 ### Added
diff --git a/gazelle/python/generate.go b/gazelle/python/generate.go
index a180ec527d..28fe063d35 100644
--- a/gazelle/python/generate.go
+++ b/gazelle/python/generate.go
@@ -490,7 +490,10 @@ func (py *Python) GenerateRules(args language.GenerateArgs) language.GenerateRes
 		result.Gen = append(result.Gen, pyTest)
 		result.Imports = append(result.Imports, pyTest.PrivateAttr(config.GazelleImportsKey))
 	}
-
+	if !cfg.CoarseGrainedGeneration() {
+		emptyRules := py.getRulesWithInvalidSrcs(cfg, args)
+		result.Empty = append(result.Empty, emptyRules...)
+	}
 	if !collisionErrors.Empty() {
 		it := collisionErrors.Iterator()
 		for it.Next() {
@@ -502,6 +505,48 @@ func (py *Python) GenerateRules(args language.GenerateArgs) language.GenerateRes
 	return result
 }
 
+// getRulesWithInvalidSrcs checks existing Python rules in the BUILD file and return the rules with invalid source files.
+// Invalid source files are files that do not exist or not a target.
+func (py *Python) getRulesWithInvalidSrcs(cfg *pythonconfig.Config, args language.GenerateArgs) (invalidRules []*rule.Rule) {
+	if args.File == nil {
+		return
+	}
+	filesMap := make(map[string]struct{})
+	for _, file := range args.RegularFiles {
+		if cfg.IgnoresFile(filepath.Base(file)) {
+			continue
+		}
+		filesMap[file] = struct{}{}
+	}
+	for _, file := range args.GenFiles {
+		filesMap[file] = struct{}{}
+	}
+
+	isTarget := func(src string) bool {
+		return strings.HasPrefix(src, "@") || strings.HasPrefix(src, "//") || strings.HasPrefix(src, ":")
+	}
+	for _, existingRule := range args.File.Rules {
+		if existingRule.Kind() != pyBinaryKind {
+			continue
+		}
+		var hasValidSrcs bool
+		for _, src := range existingRule.AttrStrings("srcs") {
+			if isTarget(src) {
+				hasValidSrcs = true
+				break
+			}
+			if _, ok := filesMap[src]; ok {
+				hasValidSrcs = true
+				break
+			}
+		}
+		if !hasValidSrcs {
+			invalidRules = append(invalidRules, newTargetBuilder(existingRule.Kind(), existingRule.Name(), args.Config.RepoRoot, args.Rel, nil).build())
+		}
+	}
+	return invalidRules
+}
+
 // isBazelPackage determines if the directory is a Bazel package by probing for
 // the existence of a known BUILD file name.
 func isBazelPackage(dir string) bool {
diff --git a/gazelle/python/testdata/remove_invalid_binary/BUILD.in b/gazelle/python/testdata/remove_invalid_binary/BUILD.in
new file mode 100644
index 0000000000..aca4df0a13
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_binary/BUILD.in
@@ -0,0 +1,11 @@
+load("@rules_python//python:defs.bzl", "py_binary")
+
+py_library(
+    name = "keep_library",
+    deps = ["//keep_binary:foo"],
+)
+py_binary(
+    name = "remove_invalid_binary",
+    srcs = ["__main__.py"],
+    visibility = ["//:__subpackages__"],
+)
diff --git a/gazelle/python/testdata/remove_invalid_binary/BUILD.out b/gazelle/python/testdata/remove_invalid_binary/BUILD.out
new file mode 100644
index 0000000000..069188f5ca
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_binary/BUILD.out
@@ -0,0 +1,6 @@
+load("@rules_python//python:defs.bzl", "py_library")
+
+py_library(
+    name = "keep_library",
+    deps = ["//keep_binary:foo"],
+)
diff --git a/gazelle/python/testdata/remove_invalid_binary/README.md b/gazelle/python/testdata/remove_invalid_binary/README.md
new file mode 100644
index 0000000000..be8a894420
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_binary/README.md
@@ -0,0 +1,3 @@
+# Remove invalid binary
+
+This test case asserts that `py_binary` should be deleted if invalid (no source files).
diff --git a/gazelle/python/testdata/remove_invalid_binary/WORKSPACE b/gazelle/python/testdata/remove_invalid_binary/WORKSPACE
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/gazelle/python/testdata/remove_invalid_binary/keep_binary/BUILD.in b/gazelle/python/testdata/remove_invalid_binary/keep_binary/BUILD.in
new file mode 100644
index 0000000000..0036c6797a
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_binary/keep_binary/BUILD.in
@@ -0,0 +1,13 @@
+load("@rules_python//python:defs.bzl", "py_binary", "py_library")
+
+py_binary(
+    name = "foo",
+    srcs = ["foo.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+py_library(
+    name = "keep_binary",
+    srcs = ["foo.py"],
+    visibility = ["//:__subpackages__"],
+)
diff --git a/gazelle/python/testdata/remove_invalid_binary/keep_binary/BUILD.out b/gazelle/python/testdata/remove_invalid_binary/keep_binary/BUILD.out
new file mode 100644
index 0000000000..0036c6797a
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_binary/keep_binary/BUILD.out
@@ -0,0 +1,13 @@
+load("@rules_python//python:defs.bzl", "py_binary", "py_library")
+
+py_binary(
+    name = "foo",
+    srcs = ["foo.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+py_library(
+    name = "keep_binary",
+    srcs = ["foo.py"],
+    visibility = ["//:__subpackages__"],
+)
diff --git a/gazelle/python/testdata/remove_invalid_binary/keep_binary/foo.py b/gazelle/python/testdata/remove_invalid_binary/keep_binary/foo.py
new file mode 100644
index 0000000000..d3b51eea8e
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_binary/keep_binary/foo.py
@@ -0,0 +1,2 @@
+if __name__ == "__main__":
+    print("foo")
diff --git a/gazelle/python/testdata/remove_invalid_binary/test.yaml b/gazelle/python/testdata/remove_invalid_binary/test.yaml
new file mode 100644
index 0000000000..e69de29bb2