The quality of randomized controlled trials (RCTs) reported in the International Journal of Impotence Research (IJIR) was analyzed. The original articles that reported RCTs and were published in the IJIR in 1997–2014 were identified by PubMed. Their methodological quality was assessed using the Jadad scale, van Tulder scale and Cochrane Collaboration Risk of Bias Tool. The review period was divided into three periods: early (1997–2002), mid (2003–2008) and late (2009–2014). The effect of study subject and presence of Institutional Review Board approval, intervention, funding and adequate allocation concealment on RCT quality was assessed. The frequency of RCT publication in the IJIR did not change over the 19-year study period. Numbers of low risk of bias articles were 1 (3.0%), 2 (4.4%) and 4 (12.1%) in the early, mid and late periods in Cochrane Collaboration Risk of Bias Tool (P = 0.04). High-quality low risk of bias RCT publication frequency increased over time. Intervention and funding significantly influenced RCT quality. Thus, the number of RCTs published in the IJIR over time has remained constant while their quality has improved. Ongoing efforts to expand the numbers of RCTs and further improve the quality of research published by the IJIR will improve clinical practice.