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Abstract Background A cluster randomised controlled trial (cRCT) performed from July 2018 to March 2019 demonstrated the clinical impact of a community pharmacist delivered minor ailment service (MAS) compared with usual pharmacist care (UC). MAS consisted of a technology-based face-to-face consultation delivered by trained community pharmacists. The consultation was guided by clinical pathways for assessment and management, and communication systems, collaboratively agreed with general practitioners. MAS pharmacists were trained and provided monthly practice support by a practice change facilitator. The objective of this study was to assess the cost utility of MAS, compared to UC. Methods Participants recruited were adult patients with symptoms suggestive of a minor ailment condition, from community pharmacies located in Western Sydney. Patients received MAS (intervention) or UC (control) and were followed-up by telephone 14-days following consultation with the pharmacist. A cost utility analysis was conducted alongside the cRCT. Transition probabilities and costs were directly derived from cRCT study data. Utility values were not available from the cRCT, hence we relied on utility values reported in the published literature which were used to calculate quality adjusted life years (QALYs), using the area under the curve method. A decision tree model was used to capture the decision problem, considering a societal perspective and a 14-day time horizon. Deterministic and probabilistic sensitivity analyses assessed robustness and uncertainty of results, respectively. Results Patients (n = 894) were recruited from 30 pharmacies and 82% (n = 732) responded to follow-up. On average, MAS was more costly but also more effective (in terms of symptom resolution and QALY gains) compared to UC. MAS patients (n = 524) gained an additional 0.003 QALYs at an incremental cost of $7.14 (Australian dollars), compared to UC (n = 370) which resulted in an ICER of $2277 (95% CI $681.49–3811.22) per QALY. Conclusion Economic findings suggest that implementation of MAS within the Australian context is cost effective. Trial registration Registered with Australian New Zealand Clinical Trials Registry (ANZCTR) and allocated the ACTRN: ACTRN12618000286246. Registered on 23 February 2018.