Much healthcare expenditure is on pharmaceutical drugs. Expenditure on medications has increased both in absolute terms, and as a proportion of total health expenditure. No previous studies have investigated the prescribing costs by general practitioners when managing patients during a weight loss intervention. This study evaluated the medication costs by individual class during a 1-year study in which 268 participants were randomized to one of two weight loss programmes, either standard care (SC) as defined by national guidelines, or a commercial provider (Weight Watchers) (CP). The baseline body mass index of participants (mean ± standard deviation) was 32.0 ± 2.5 kg m , their body weight was 87.5 ± 11.8 kg, and age 47.4 ± 11.7 years. Weight loss for the SC and CP groups was -2.6 and -6.1 kg, respectively (between group difference; P < 0.0001). The greater weight loss in the CP group compared to SC was accompanied by larger reductions in waist circumference and fat mass. The CP group also had significantly greater improvements than SC in high-density lipoprotein cholesterol. Despite SC participants being prescribed and spending more on medications than the CP group with no better weight or metabolic outcomes, this was not of statistical significance. For both groups the highest proportion of prescriptions (≥30% of medications) was for control of risk factors for cardiovascular disease. In conclusion, this study indicates that obesity treatment via a shared care approach with a CP results in greater weight loss and some better clinical outcomes, but despite lower medication costs overall, this was not significant when compared to SC treatment.