diff --git a/utbot-core/src/main/kotlin/org/utbot/common/StopWatch.kt b/utbot-core/src/main/kotlin/org/utbot/common/StopWatch.kt
index 1c355317f9..1ff1b149fa 100644
--- a/utbot-core/src/main/kotlin/org/utbot/common/StopWatch.kt
+++ b/utbot-core/src/main/kotlin/org/utbot/common/StopWatch.kt
@@ -28,12 +28,19 @@ class StopWatch {
             startTime = System.currentTimeMillis()
         }
     }
-    
-    fun stop() {
+
+    /**
+     * @param compensationMillis the duration in millis that should be subtracted from [elapsedMillis] to compensate
+     * for stopping and restarting [StopWatch] taking some time, can also be used to compensate for some activities,
+     * that are hard to directly detect (e.g. class loading).
+     *
+     * NOTE: [compensationMillis] will never cause [elapsedMillis] become negative.
+     */
+    fun stop(compensationMillis: Long = 0) {
         lock.withLockInterruptibly {
-            startTime?.let {
-                elapsedMillis += (System.currentTimeMillis() - it)
-                startTime = null
+            startTime?.let { startTime ->
+                elapsedMillis += ((System.currentTimeMillis() - startTime) - compensationMillis).coerceAtLeast(0)
+                this.startTime = null
             }
         }
     }
diff --git a/utbot-instrumentation/src/main/kotlin/org/utbot/instrumentation/agent/DynamicClassTransformer.kt b/utbot-instrumentation/src/main/kotlin/org/utbot/instrumentation/agent/DynamicClassTransformer.kt
index c3e83d4694..e9ba0651ff 100644
--- a/utbot-instrumentation/src/main/kotlin/org/utbot/instrumentation/agent/DynamicClassTransformer.kt
+++ b/utbot-instrumentation/src/main/kotlin/org/utbot/instrumentation/agent/DynamicClassTransformer.kt
@@ -35,7 +35,9 @@ class DynamicClassTransformer : ClassFileTransformer {
         classfileBuffer: ByteArray
     ): ByteArray? {
         try {
-            UtContext.currentContext()?.stopWatch?.stop()
+            // since we got here we have loaded a new class, meaning program is not stuck and some "meaningful"
+            // non-repeating actions are performed, so we assume that we should not time out for then next 65 ms
+            UtContext.currentContext()?.stopWatch?.stop(compensationMillis = 65)
             val pathToClassfile = protectionDomain.codeSource?.location?.toURI()?.let(Paths::get)?.absolutePathString()
             return if (pathToClassfile in pathsToUserClasses ||
                 packsToAlwaysTransform.any(className::startsWith)