In this paper, Signal to noise ratio estimation in Orthogonal Frequency Division Multiplexing based cooperative communication system is proposed. SNR estimation is needed for the best and optimized recovery of the data at the receiver and been used for adaptive control and coding purposes in the communication systems. The cooperative relay communication system takes advantage of the broadcast nature of the wireless channel to improve the communication between the source node and a destination node with the aid of one or more relay nodes. The system harnesses the new form of spatial diversity and combat multipath fading, thereby improving the spectral efficiency, and reducing the transmission error, system outages, and transmission power. OFDM modulated system is used for the implementation of cooperative communication system in MATLAB®. The estimator makes use of two identical halves property of time synchronization preamble used in OFDM systems and relies on autocorrelation of the same. The current estimator is compared with SISO SNR estimation method in-terms of normalized mean square error (NMSE) and estimated SNR. Results shows that the proposed estimator provides enhanced performance in SNR estimation as compared to SISO systems.