Similarly to many scientific disciplines, neuroscience has increasingly attempted to confront pervasive gender imbalances. Although publishing and conference participation are often highlighted, recent research has called attention to the prevalence of gender imbalance in citations. Because of the downstream effects of citations on visibility and career advancement, understanding the role of gender in citation practices is vital for addressing scientific inequity. Here, we investigate whether gendered patterns are present in neuroscience citations. 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 unrelated to referencing. Importantly, we show that this imbalance is driven largely by the citation practices of men and is increasing over time as the field diversifies. We assess and discuss possible mechanisms and consider how researchers might approach these issues in their own work.