This paper considers two-machine Flow shop scheduling problem while there is ineligible transportation lags in production procedure. There is one transporter to convey semi-finished jobs between machines, and another transporter to deliver finished jobs to the warehouse (customers). The problem is formulated as a mixed integer linear programming (MILP) model to minimize the makespan as an objective function. To solve the problem in an efficient way, two heuristic algorithms are also developed. Furthermore, five lower bounds are proposed and computational experiments are carried out to verify the effectiveness of the proposed lower bounds and heuristic algorithms. The results show the performance of the heuristics to deal with medium and large size problems.