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. Utilizing data from five top neuroscience journals, we indeed find that reference lists tend to include more papers with men as first and last author than would be expected if gender was 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 with time despite greater diversity in the academy. We develop a co-authorship network to determine the degree to which homophily in researchers' social networks explains gendered citation practices and we find that men tend to overcite other men even when their social networks are representative of the field. We discuss possible mechanisms and consider how individual researchers might incorporate these findings into their own referencing practices.