diff --git a/bindings/pyroot/pythonizations/test/ml_dataloader.py b/bindings/pyroot/pythonizations/test/ml_dataloader.py
index 491bcaf8ae5aa..748d3517c5d73 100644
--- a/bindings/pyroot/pythonizations/test/ml_dataloader.py
+++ b/bindings/pyroot/pythonizations/test/ml_dataloader.py
@@ -4570,6 +4570,44 @@ def test16_vector_padding(self):
             self.teardown_file(self.file_name5)
             raise
 
+    def test17_shuffled_split_varies_with_seed(self):
+        self.create_file1()
+        self.create_file2()
+
+        try:
+            df1 = ROOT.RDataFrame(self.tree_name, self.file_name1)
+            df2 = ROOT.RDataFrame(self.tree_name, self.file_name2)
+
+            dl1 = ROOT.Experimental.ML.RDataLoader(
+                [df1, df2],
+                batch_size=3,
+                target="b2",
+                shuffle=True,
+                drop_remainder=False,
+                set_seed=42,
+            )
+
+            dl2 = ROOT.Experimental.ML.RDataLoader(
+                [df1, df2],
+                batch_size=3,
+                target="b2",
+                shuffle=True,
+                drop_remainder=False,
+                set_seed=43,
+            )
+
+            _, gen_val1 = dl1.train_test_split(0.4)
+            _, gen_val2 = dl2.train_test_split(0.4)
+
+            val_1_collected = sorted([v for x, y in gen_val1.as_numpy() for v in x.flatten().tolist()])
+            val_2_collected = sorted([v for x, y in gen_val2.as_numpy() for v in x.flatten().tolist()])
+
+            self.assertNotEqual(val_1_collected, val_2_collected)
+
+        finally:
+            self.teardown_file(self.file_name1)
+            self.teardown_file(self.file_name2)
+
 
 class DataLoaderRandomUndersampling(unittest.TestCase):
     file_name1 = "major.root"
diff --git a/tree/ml/inc/ROOT/ML/RClusterLoader.hxx b/tree/ml/inc/ROOT/ML/RClusterLoader.hxx
index fabad80b3be33..090b097923c1a 100644
--- a/tree/ml/inc/ROOT/ML/RClusterLoader.hxx
+++ b/tree/ml/inc/ROOT/ML/RClusterLoader.hxx
@@ -227,18 +227,27 @@ public:
          // --- Shuffled path
          // Every cluster contributes a prefix to training and a suffix to validation.
          // Cost: Each cluster is read twice per epoch, only when validation split is more than 0.
-         // TODO(staider) Swicth between prefix or suffix for validation randomly per cluster
+         // We generate a random boolean value to decide whether the training set gets the prefix
+         // or suffix of each cluster to ensure better shuffling across runs when splitting.
+         std::mt19937 g(fSetSeed);
+         std::uniform_int_distribution<int> coin(0, 1);
+
          for (const RClusterRange &c : fAllClusters) {
             const std::size_t sz = c.GetNumEntries();
             const std::size_t trainSz = static_cast<std::size_t>((1.0f - fValidationSplit) * sz);
             const std::size_t valSz = sz - trainSz;
 
+            // Randomly assign prefix or suffix to training
+            bool trainIsPrefix = coin(g);
+            const uint64_t trainStart = trainIsPrefix ? c.start : c.start + static_cast<std::uint64_t>(valSz);
+            const uint64_t valStart = trainIsPrefix ? c.start + static_cast<std::uint64_t>(trainSz) : c.start;
+
             if (trainSz > 0) {
-               fTrainingClusters.push_back({c.rdfIdx, c.start, c.start + static_cast<std::uint64_t>(trainSz)});
+               fTrainingClusters.push_back({c.rdfIdx, trainStart, trainStart + static_cast<std::uint64_t>(trainSz)});
                fNumTrainingEntries += trainSz;
             }
             if (valSz > 0) {
-               fValidationClusters.push_back({c.rdfIdx, c.start + static_cast<std::uint64_t>(trainSz), c.end});
+               fValidationClusters.push_back({c.rdfIdx, valStart, valStart + static_cast<std::uint64_t>(valSz)});
                fNumValidationEntries += valSz;
             }
          }
@@ -392,14 +401,29 @@ public:
             std::min(static_cast<std::size_t>(totalFiltered * (1.0f - fValidationSplit)), trainRemaining);
          const std::size_t valCount = totalFiltered - trainCount;
 
+         bool trainIsPrefix = true;
+         if (fShuffle) {
+            // If shuffling is enabled, we generate a random boolean value to decide whether the training set
+            // gets the prefix or suffix of each cluster to ensure better shuffling across runs when splitting.
+            std::mt19937 g(fSetSeed + fAccumulatedFilteredForTrain); // vary per cluster
+            std::uniform_int_distribution<int> coin(0, 1);
+            trainIsPrefix = coin(g);
+         }
+
          // The boundary is the raw entry index of the first entry assigned to validation.
          // Stable across epochs since the same filter always produces the same ordered entries.
-         const std::uint64_t boundary = (valCount > 0) ? rdfEntries[trainCount] : endRow;
+         const std::uint64_t trainBoundaryEntry = trainIsPrefix ? rdfEntries[trainCount] : rdfEntries[valCount];
+         const std::uint64_t boundary = (valCount > 0) ? trainBoundaryEntry : endRow;
+
+         const std::uint64_t trainStart = trainIsPrefix ? startRow : boundary;
+         const std::uint64_t trainEnd = trainIsPrefix ? boundary : endRow;
+         const std::uint64_t valStart = trainIsPrefix ? boundary : startRow;
+         const std::uint64_t valEnd = trainIsPrefix ? endRow : boundary;
 
          if (trainCount > 0)
-            fTrainingClusters.push_back({rdfIdx, startRow, boundary, trainCount});
+            fTrainingClusters.push_back({rdfIdx, trainStart, trainEnd, trainCount});
          if (valCount > 0)
-            fValidationClusters.push_back({rdfIdx, boundary, endRow, valCount});
+            fValidationClusters.push_back({rdfIdx, valStart, valEnd, valCount});
 
          fAccumulatedFilteredForTrain += trainCount;
          return trainCount;