Background Full separation of prescribing and dispensing remains a subject of heated debate in Malaysia. Understanding public perception on the issue in order to garner public support is crucial in efforts to enact a change in policy. Aim This study assessed public perception of the separation of prescribing and dispensing in Malaysia within the context of the public's knowledge of the professional roles of pharmacists, awareness of the issue and the current healthcare system. Methods This cross‐sectional study used a validated self‐administered questionnaire, which was administered to random members of the public. Descriptive and inferential statistics were used to analyse the data. Results In all, 495 respondents participated in the study (response rate 61.9%). Most respondents were aware of pharmacists’ roles in educating patients (84.6%), checking prescriptions (65.9%) and dispensing medicines (85.1%). Most respondents (86.7%) agreed that pharmacists were more knowledgeable than physicians regarding medications and were aware that separation of prescribing and dispensing occurs in other developed countries (67.5%) and the public sector (70.9%). Approximately half of all respondents (52.5%) agreed that full separation of prescribing and dispensing should be implemented, with a higher level of agreement observed among respondents who were younger (68.0%), had tertiary education (69.8%), had a background in health sciences (71.7%) or were aware of the policy being practiced elsewhere (76.3%). However, only 28.5% of all respondents agreed that Malaysia was ready to implement a separation policy. This low level of agreement was consistent across all respondent groups except pharmacists, of which a slight majority (53.7%) agreed. Conclusions Approximately half the respondents agreed that full separation of prescribing should be implemented, but a significantly smaller proportion agreed that the country is ready to implement a separation system.