A wide range of web-based applications uses the Transmission Control Protocol (TCP) to ensure network resources are shared efficiently and fairly. As wired and wireless networks have become more complex, various end-to-end Congestion Control (CC) schemes have been developed, offering solutions through their proposed TCP variants. Network tomography, a powerful analytical tool, offers a unique perspective by measuring end-to-end performance to estimate internal network parameters, including latency. This estimation capability proves valuable, especially in cases where precise protocol performance evaluation is essential. TCP protocol can be improved significantly by properly estimating RTT time. It has resulted in better network conditions and improved reliability, as well as a higher level of user satisfaction. In this study, we propose a method to infer the link delay using network tomography and then adjust the RTT based on the delay estimation obtained in the previous step. Simulation results performed using the NS2 software show that the proposed method significantly improves the TCP protocol's Round-Trip Time (RTT) estimation by more than 15%. It reduces congestion, improves information transfer efficiency, and ensures the highest level of service in the network.