Loss of system stability, high transmission loss, voltage limit violations, inability to utilize transmission line capability up to the thermal limit and cascade tripping are some of the operational problems in a power system. Flexible Alternating Current Transmission Systems (FACTS) is a recent technological development in electrical power system that has come up to alleviate the said operational problems. The development of SE algorithm suitable for power systems embedded with the FACTS controller, Unified Power Flow Controllers (UPFC), is more realistic. In this paper, elements of the state estimation Jacobian matrix are obtained considering the power flow measurements in the network elements. These elements are processed one-by-one and the Jacobian matrix H is updated suitably in a simple manner. The constructed Jacobian matrix H is integrated with Weight Least Square method to estimate the state variables. The suggested procedure is successfully tested on IEEE standard systems.