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Background Regulatory inspection of private drug shops in Uganda is a mandate of the Ministry of Health carried out by the National Drug Authority. This study evaluated how this mandate is being carried out at national, district, and drug shop levels. Specifically, perspectives on how the inspection is done, who does it, and challenges faced were sought from inspectors and drug sellers. Methods Six key informant interviews (KIIs) were held with inspectors at the national and district level, while eight focus group discussions (FGDs) were conducted among nursing assistants, and two FGDs were held with nurses. The study appraised current methods of inspecting drug sellers against national professional guidelines for licensing and renewal of class C drug shops in Uganda. Transcripts were managed using Atlas ti version 7 (ATLAS.ti GmbH, Berlin) data management software where the thematic content analysis was done. Results Five themes emerged from the study: authoritarian inspection, delegated inspection, licensing, training, and bribes. Under authoritarian inspection, drug sellers decried the high handedness used by inspectors when found with expired or no license at all. For delegated inspection, drug sellers said that sometimes, inspectors send health assistants and sub-county chiefs for inspection visits. This cadre of people is not recognized by law as inspectors. Inspectors trained drug sellers on how to organize their drug shops better and how to use new technologies such as rapid diagnostic tests (RDTs) in diagnosing malaria. Bribes were talked about mostly by nursing assistants who purported that inspectors were not interested in inspection per se but collecting illicit payments from them. Inspectors said that the facilitation they received from the central government were inadequate for a routine inspection. Conclusion The current method of inspecting drug sellers is harsh and instills fear among drug sellers. There is a need to establish a well-recognized structure of inspection as well as establish channels of dialogue between inspectors and drug sellers if meaningful compliance is to be achieved. The government also needs to enhance both human and financial resources if meaningful inspection of drug sellers is to take place.