We showed previously that neonatal isolation (ISO) enhances acquisition of cocaine self-administration in adult male rats without altering acquisition of food responding. Female rats show poorer performance in learning tasks and are differentially affected by stress compared to male rats. Thus, we investigated whether ISO alters acquisition of operant responding for cocaine and food in female rats with comparison to male rats. Litters were subjected to ISO or were non-handled (NH). Activity levels were assessed in adult rats. Then, rats were implanted with jugular catheters and allowed to self-administer cocaine under a fixed-ratio 1 (FR1) schedule of reinforcement using an escalating dose presentation procedure. Cocaine intake, discrimination of active versus inactive levers, and ineffective active lever responses were tabulated. Effects of non-contingent cocaine infusions (primes) and increasing FR on responding were then assessed. Other rats were allowed to lever press for food under an FR1 schedule (10 s time-out). ISO enhanced acquisition of operant responding for food and cocaine in female rats. The latter was demonstrated by better lever discrimination, emission of fewer ineffective responses, and superior performance in response to primes. Yet, NH females ingested more cocaine than ISO females during the initial acquisition phase. In male rats, ISO enhanced acquisition of cocaine self-administration but not food responding. Activity levels were unaffected by ISO or gender. These data confirm and extend our previous findings demonstrating the enduring effects of ISO on adult self-administration behavior and emphasize the importance of measuring behavioral patterns versus intake in acquisition studies.