diff --git a/yorkie/src/main/kotlin/dev/yorkie/util/SplayTreeSet.kt b/yorkie/src/main/kotlin/dev/yorkie/util/SplayTreeSet.kt
index 8dc67a205..b65c98f8b 100644
--- a/yorkie/src/main/kotlin/dev/yorkie/util/SplayTreeSet.kt
+++ b/yorkie/src/main/kotlin/dev/yorkie/util/SplayTreeSet.kt
@@ -73,7 +73,7 @@ internal class SplayTreeSet<V>(
      */
     fun indexOf(value: V?): Int {
         val node = valueToNodes[value]
-        if (node == null || !node.hasLinks) {
+        if (node == null || node !== root && !node.hasLinks) {
             return -1
         }
         var index = 0
diff --git a/yorkie/src/test/kotlin/dev/yorkie/util/SplayTreeSetTest.kt b/yorkie/src/test/kotlin/dev/yorkie/util/SplayTreeSetTest.kt
index 8723bcf13..f382f5360 100644
--- a/yorkie/src/test/kotlin/dev/yorkie/util/SplayTreeSetTest.kt
+++ b/yorkie/src/test/kotlin/dev/yorkie/util/SplayTreeSetTest.kt
@@ -99,6 +99,15 @@ class SplayTreeSetTest {
         assertIfRangeCutOff(nodes, 3..7)
     }
 
+    @Test
+    fun `should handle indexOf correctly with single node`() {
+        val node = Node("A")
+        target.insert(node)
+        assertEquals(0, target.indexOf(node))
+        target.delete(node)
+        assertEquals(-1, target.indexOf(node))
+    }
+
     private fun assertIfRangeCutOff(nodes: List<Node>, targetRange: IntRange) {
         assertEquals(
             0,