The present disclosure relates to system(s) and method(s) for deploying a java agent in runtime. The method creates a .WAR file associated with a java agent. The .WAR file corresponds to a servlet configured to run the java agent. The method further determines an existence of a reference holder class in a bootstrap class loader using the servlet. Based on the determination of the reference holder class, the method connects the servlet to a Java Virtual Machine (JVM). The servlet is connected to the JVM using an open source library. Further, the method deploys the java agent in real-time based on a deployment of a bootstrap class using the servlet. The bootstrap class holds a reference to the java agent. The bootstrap class acts as the reference holder class.