diff --git a/src/python/pants/core/util_rules/system_binaries.py b/src/python/pants/core/util_rules/system_binaries.py
index f59c13e8326..01a92a97376 100644
--- a/src/python/pants/core/util_rules/system_binaries.py
+++ b/src/python/pants/core/util_rules/system_binaries.py
@@ -11,6 +11,7 @@
 import subprocess
 from dataclasses import dataclass
 from enum import Enum
+from itertools import groupby
 from textwrap import dedent  # noqa: PNT20
 from typing import Iterable, Mapping, Sequence
 
@@ -243,6 +244,21 @@ def for_paths(
         *paths: BinaryPath,
         rationale: str,
     ) -> BinaryShimsRequest:
+        # Remove any duplicates (which may result if the caller merges `BinaryPath` instances from multiple sources)
+        # and also sort to ensure a stable order for better caching.
+        paths = tuple(sorted(set(paths), key=lambda bp: bp.path))
+
+        # Then ensure that there are no duplicate paths with mismatched content.
+        duplicate_paths = set()
+        for path, group in groupby(paths, key=lambda x: x.path):
+            if len(list(group)) > 1:
+                duplicate_paths.add(path)
+        if duplicate_paths:
+            raise ValueError(
+                "Detected duplicate paths with mismatched content at paths: "
+                f"{', '.join(sorted(duplicate_paths))}"
+            )
+
         return cls(
             paths=paths,
             rationale=rationale,
diff --git a/src/python/pants/core/util_rules/system_binaries_test.py b/src/python/pants/core/util_rules/system_binaries_test.py
index e7d5d04542d..1d8d8e19667 100644
--- a/src/python/pants/core/util_rules/system_binaries_test.py
+++ b/src/python/pants/core/util_rules/system_binaries_test.py
@@ -176,3 +176,37 @@ def test_binary_shims_paths(rule_runner: RuleRunner, tmp_path: Path) -> None:
         ),
         binary_shim.content.decode(),
     )
+
+
+def test_merge_and_detection_of_duplicate_binary_paths() -> None:
+    # Test merge of duplicate paths where content hash is the same.
+    shims_request_1 = BinaryShimsRequest.for_paths(
+        BinaryPath("/foo/bar", "abc123"),
+        BinaryPath("/abc/def/123", "def456"),
+        BinaryPath("/foo/bar", "abc123"),
+        rationale="awesomeness",
+    )
+    assert shims_request_1.paths == (
+        BinaryPath("/abc/def/123", "def456"),
+        BinaryPath("/foo/bar", "abc123"),
+    )
+
+    # Test detection of duplicate pahs with differing content hashes. Exception should be thrown.
+    with pytest.raises(ValueError, match="Detected duplicate paths with mismatched content"):
+        _ = BinaryShimsRequest.for_paths(
+            BinaryPath("/foo/bar", "abc123"),
+            BinaryPath("/abc/def/123", "def456"),
+            BinaryPath("/foo/bar", "xyz789"),
+            rationale="awesomeness",
+        )
+
+    # Test paths with no duplication.
+    shims_request_2 = BinaryShimsRequest.for_paths(
+        BinaryPath("/foo/bar", "abc123"),
+        BinaryPath("/abc/def/123", "def456"),
+        rationale="awesomeness",
+    )
+    assert shims_request_2.paths == (
+        BinaryPath("/abc/def/123", "def456"),
+        BinaryPath("/foo/bar", "abc123"),
+    )