Introduction Adolescent girls and young women (AGYW) are a priority population for pre‐exposure prophylaxis (PrEP), a highly effective HIV prevention method. However, effective PrEP use among AGYW has been low. Interventions to support PrEP effective use may improve pill‐taking. Affordability of PrEP programs depends on their cost. We, therefore, evaluated the cost of community‐based PrEP with effective use counselling. Methods Cost data from a randomized controlled trial were used to evaluate the cost of PrEP provision with effective use counselling offered to AGYW through community‐based HIV testing platforms between November 2018 and November 2019. AGYW were randomized to receive (1) group‐based community health club effective use counselling, (2) individualized effective use counselling or (3) community‐based PrEP dispensary. Task shifting of effective use counselling from nurses to trained lay counsellors was implemented in groups 1 and 2. Personnel costs were estimated from time‐and‐motion observations and staff interviews. Expenditure and ingredients‐based approaches were used to estimate costs for medical and non‐medical supplies. Results In total, 603 AGYW initiated PrEP and accrued a total of 1280 months on PrEP. Average cost per person‐month on PrEP with group‐based community health club, individualized effective use counselling and community‐based PrEP dispensary under the Department of Health scenario were similar and high (USD $55.32, $55.65 and $55.46, respectively) due to low PrEP client volume observed in the clinical trial. Increasing client volume (scaled Department of Health scenario) reduced cost per‐person month estimates to USD $15.48, $26.40 and $13.99, respectively. Conclusions As designed, individualized effective use counselling increased the cost of standard‐of‐care PrEP delivery by 89%, group‐based community health effective use counselling increased the cost of standard‐of‐care PrEP delivery by 11%. These estimates can inform cost‐effectiveness and budget impact analysis for PrEP provision with effective use counselling services.