In many industrial setups, setup time on machines during the processing of given jobs in flow shop has great impact on the objective considered; hence the setups need to be taken separately during the process. Two types of setups exist in flow shop scheduling problem namely sequence-independent and sequence-dependent setup times. Scheduling of jobs with sequence-dependent setup times in flow shop scheduling is the most complicated case in the theory of scheduling. The main concern in this paper is the sequence-dependent setup time in which the setup time depends on the job type to be done and just completed. In this paper, a heuristic algorithm for solving bi-criteria flow shop problem with sequencedependent setup times is proposed. The bi-criteria objective considered is the minimization of the operational cost of machines subject to minimum makespan in a flow shop whenever the setup times on machines are sequence-dependent. As the problem is NP-hard, the proposed heuristic algorithm finds the latest time at which the machines should start so as to reduce their operating time and hence the operational cost subject to minimum makespan. The problem discussed in the paper can easily be seen in the industrial setups where expensive machinery is in operation or it is difficult to start or stop the machines due to operations technical limitations. The proposed algorithm makes use of famous NEH algorithm with a new tie-breaking rule. The tie-breaking rule breaks the tie for sequences with equal makespan during the run of algorithm. The starting of machines at latest time reduces the operating time and hence the operational cost of machines. The proposed heuristic algorithm when applied to given set of data reduced the total operational cost of machines from 2166 units to 2040 units subject to minimum makespan 90 units thereby reducing the total cost of machines by 126 units. A numerical example is also given to substantiate the algorithm.