diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/InMemoryFileIndex.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/InMemoryFileIndex.scala
index 44d31131e9c6d..8920ff88be519 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/InMemoryFileIndex.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/InMemoryFileIndex.scala
@@ -101,7 +101,7 @@ class InMemoryFileIndex(
   }
 
   override def equals(other: Any): Boolean = other match {
-    case hdfs: InMemoryFileIndex => rootPaths.toSet == hdfs.rootPaths.toSet
+    case hdfs: InMemoryFileIndex => rootPaths.sorted == hdfs.rootPaths.sorted
     case _ => false
   }
 
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/datasources/FileIndexSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/datasources/FileIndexSuite.scala
index 9ac61f0cee5fc..54403ea99c813 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/datasources/FileIndexSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/datasources/FileIndexSuite.scala
@@ -554,6 +554,30 @@ class FileIndexSuite extends SharedSparkSession {
     assert(FileIndexOptions.isValidOption("modifiedafter"))
     assert(FileIndexOptions.isValidOption("pathglobfilter"))
   }
+
+  test("SPARK-52339: Correctly compare root paths") {
+    withTempDir { dir =>
+      val file1 = new File(dir, "text1.txt")
+      stringToFile(file1, "text1")
+      val file2 = new File(dir, "text2.txt")
+      stringToFile(file2, "text2")
+      val path1 = new Path(file1.getCanonicalPath)
+      val path2 = new Path(file2.getCanonicalPath)
+
+      val schema = StructType(Seq(StructField("a", StringType, false)))
+
+      // Verify that the order of paths doesn't matter
+      val fileIndex1a = new InMemoryFileIndex(spark, Seq(path1, path2), Map.empty, Some(schema))
+      val fileIndex1b = new InMemoryFileIndex(spark, Seq(path2, path1), Map.empty, Some(schema))
+      assert(fileIndex1a == fileIndex1b)
+
+      // Verify that a different number of paths does matter
+      val fileIndex2a = new InMemoryFileIndex(spark, Seq(path1, path1), Map.empty, Some(schema))
+      val fileIndex2b = new InMemoryFileIndex(spark, Seq(path1, path1, path1),
+        Map.empty, Some(schema))
+      assert(fileIndex2a != fileIndex2b)
+    }
+  }
 }
 
 object DeletionRaceFileSystem {