Circadian locomotor activity patterns in Drosophila exhibit distinct sexual dimorphism in the phase of the rhythm. Since central complex is involved in integration of visual inputs and acts as higher order centre for locomotion, we investigated the presence of peripheral circadian clocks in the central complex and the possible substrate for sexually dimorphic locomotor activity patterns. Misexpression of positive regulators of circadian clock i.e., CLOCK and CYCLE in the central complex led to an altered locomotor pattern under periodic conditions but did not change the overt rhythmicity in the absence of time cues. Evening activity peak was abolished and a reduction in total activity was observed upon inducing dominant negative version of CLOCK in the central complex. Interestingly, we found that females failed to develop when a dominant negative version of CLOCK is expressed using one of the central complex drivers. Our study identified the involvement of central complex at cellular network level and the circadian activator CLOCK at the molecular level in mediating sexually dimorphic development and locomotor behavior of male flies.