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Background Yaws is a treponemal infection that was almost eradicated fifty years ago; however, the disease has re-emerged in a number of countries including Ghana. A single-dose of intramuscular benzathine penicillin has been the mainstay of treatment for yaws. However, intramuscular injections are painful and pose safety and logistical constraints in the poor areas where yaws occurs. A single center randomized control trial (RCT) carried out in Papua New Guinea in 2012 demonstrated the efficacy of a single-dose of oral azithromycin for the treatment of yaws. In this study, we also compared the efficacy of a single oral dose of azithromycin as an alternative to intramuscular benzathine penicillin for the treatment of the disease in another geographic setting. Methodology We conducted an open-label, randomized non-inferiority trial in three neighboring yaws-endemic districts in Southern Ghana. Children aged 1–15 years with yaws lesions were assigned to receive either 30mg/kg of oral azithromycin or 50,000 units/kg of intramuscular benzathine penicillin. The primary end point was clinical cure rate, defined as a complete or partial resolution of lesions 3 weeks after treatment. The secondary endpoint was serological cure, defined as at least a 4-fold decline in baseline RPR titre 6 months after treatment. Non- inferiority of azithromycin treatment was determined if the upper bound limit of a 2 sided 95% CI was less than 10%. Findings The mean age of participants was 9.5 years (S.D.3.1, range: 1–15 years), 247(70%) were males. The clinical cure rates were 98.2% (95% CI: 96.2–100) in the azithromycin group and 96.9% (95% CI: 94.1–99.6) in the benzathine penicillin group. The serological cure rates at 6 months were 57.4% (95% CI: 49.9–64.9) in the azithromycin group and 49.1% (95% CI: 41.2–56.9) in the benzathine penicillin group, thus achieving the specified criteria for non-inferiority. Conclusions A single oral dose of azithromycin, at a dosage of 30mg/kg, was non-inferior to a single dose of intramuscular benzathine penicillin for the treatment of early yaws among Ghanaian patients, and provides additional support for the WHO policy for use of oral azithromycin for the eradication of yaws in resource-poor settings. Trial Registration Pan African Clinical Trials Registry PACTR2013030005181 http://www.pactr.org/, Author Summary Yaws is a tropical infection caused by a bacterium closely related to that which causes syphilis. It is transmitted from person to person through skin to skin contact and often causes papillomatous and ulcerative skin lesions, usually in young children. Without treatment, it can lead to deformities and disabilities. In the past, treatment of cases and their contacts and mass treatment of whole communities has been conducted using single doses of long acting penicillin. This treatment is inexpensive and does not pose a problem with adherence. However, the injections are painful and make it difficult to gain the cooperation of children. In addition, it requires trained health workers to safely administer treatment in poor-resource settings where yaws commonly occurs. In this study one group of children aged 1–15 years with clinically and serologically confirmed yaws received the standard treatment of a single injection of benzathine penicillin. A second group of children were treated with a single dose of oral azithromycin. The children were followed up at 3 weeks to assess healing of lesions, and at 3 and 6 months respectively to monitor serological indicators of infection. Our conclusion is that single dose oral azithromycin is as effective as a single injection of benzathine penicillin for the treatment of early yaws in Ghana and confirms the findings of a previous study undertaken in Papua New Guinea.