Like many scientific disciplines, neuroscience has increasingly attempted to confront pervasive gender imbalances within the field. While much of the conversation has centered around publishing and conference participation, recent research in other fields has called attention to the prevalence of gender bias in citation practices. Because of the downstream effects that citations can have on visibility and career advancement, understanding and eliminating gender bias in citation practices is vital for addressing inequity in a scientific community. In this study, we sought to determine whether there is evidence of gender bias in the citation practices of neuroscientists. Using data from five top neuroscience journals, we find that reference lists tend to include more papers with men as first and last author than would be expected if gender were not a factor in referencing. Importantly, we show that this overcitation of men and undercitation of women is driven largely by the citation practices of men, and is increasing over time as the field becomes more diverse. We develop a co-authorship network to assess homophily in researchers social networks, and we find that men tend to overcite men even when their social networks are representative. We discuss possible mechanisms and consider how individual researchers might address these findings in their own practices.