Flow shop scheduling problems relates the generation of appropriate sequencing for processing of N machines in compliance with given processing sequence orders. Due to costing requirements and time delivery constraints, continuous flow of processing tasks is desired within completion time and with minimum of due date time. Viewing as optimization problem and focusing on two machines, this research aims to develop a new Simulated Annealing based scheduling algorithm, called SA2M, for flow shop problem. The developed algorithm will be compared to the existing Johnson’s algorithm in term of its costs. It is expected that the developed algorithm will perform well if not a par with Johnson’s algorithm.