The use of bicycle helmets to prevent or reduce serious head injuries is well established. However, it is unclear how to effectively promote helmet use, particularly in the context of bicycle-sharing programs. The need to determine rates of helmet use specifically among users of bicycle-sharing programs and understand if certain characteristics, such as time of day, affect helmet use, is imperative if effective promotion and/or legislative efforts addressing helmet use are to be developed. We estimated the prevalence of helmet use among a sample of Citi Bike program users in New York City. A total of 1,054 cyclists were observed over 44 h and across the 22 busiest Citi Bike locations. Overall, 85.3% (95% CI 82.2, 88.4%) of the cyclists observed did not wear a helmet. Rates of helmet non-use were also consistent whether cyclists were entering or leaving the docking station, among cyclists using the Citi Bikes earlier versus later in the day, and among cyclists using the Citi Bikes on weekends versus weekdays. Improved understanding about factors that facilitate and hinder helmet use is needed to help reduce head injury risk among users of bicycle sharing programs.