diff --git a/tools/bash/runfiles/runfiles.bash b/tools/bash/runfiles/runfiles.bash
index d6e142b8d4690e..e2d0f5eb05be92 100644
--- a/tools/bash/runfiles/runfiles.bash
+++ b/tools/bash/runfiles/runfiles.bash
@@ -235,7 +235,14 @@ function runfiles_current_repository() {
     # uses / as the path separator even on Windows.
     local -r normalized_caller_path="$(echo "$caller_path" | sed 's|\\\\*|/|g')"
     local -r escaped_caller_path="$(echo "$normalized_caller_path" | sed 's/[^-A-Za-z0-9_/]/\\&/g')"
-    rlocation_path=$(__runfiles_maybe_grep -m1 "^[^ ]* ${escaped_caller_path}$" "${RUNFILES_MANIFEST_FILE}" | cut -d ' ' -f 1)
+    if [[ "$(uname -o)" == Msys ]]; then
+      # Windows paths are case insensitive and Bazel and MSYS2 capitalize differently, so we can't
+      # assume that all paths are in the same native case.
+      local -r grep_arg="-i"
+    else
+      local -r grep_arg=
+    fi
+    rlocation_path=$(__runfiles_maybe_grep "$grep_arg" -m1 "^[^ ]* ${escaped_caller_path}$" "${RUNFILES_MANIFEST_FILE}" | cut -d ' ' -f 1)
     if [[ -z "$rlocation_path" ]]; then
       if [[ "${RUNFILES_LIB_DEBUG:-}" == 1 ]]; then
         echo >&2 "ERROR[runfiles.bash]: runfiles_current_repository($idx): ($normalized_caller_path) is not the target of an entry in the runfiles manifest ($RUNFILES_MANIFEST_FILE)"