Not wearing a helmet, not properly strapping the helmet on, or wearing a substandard helmet increases the risk of fatalities and injuries in motorcycle crashes. This research examines the differences in motorcycle crash injury severity considering crashes involving the compliance with and defiance of helmet use by motorcycle riders and highlights the temporal variation in their impact. Three-year (2017–2019) motorcycle crash data were collected from RESCUE 1122, a provincial emergency response service for Rawalpindi, Pakistan. The available crash data include crash-specific information, vehicle, driver, spatial and temporal characteristics, roadway features, and traffic volume, which influence the motorcyclist’s injury severity. A random parameters logit model with heterogeneity in means and variances was evaluated to predict critical contributory factors in helmet-wearing and non-helmet-wearing motorcyclist crashes. Model estimates suggest significant variations in the impact of explanatory variables on motorcyclists’ injury severity in the case of compliance with and defiance of helmet use. For helmet-wearing motorcyclists, key factors significantly associated with increasingly severe injury and fatal injuries include young riders (below 20 years of age), female pillion riders, collisions with another motorcycle, large trucks, passenger car, drivers aged 50 years and above, and drivers being distracted while driving. In contrast, for non-helmet-wearing motorcyclists, the significant factors responsible for severe injuries and fatalities were distracted driving, the collision of two motorcycles, crashes at U-turns, weekday crashes, and drivers above 50 years of age. The impact of parameters that predict motorcyclist injury severity was found to vary dramatically over time, exhibiting statistically significant temporal instability. The results of this study can serve as potential motorcycle safety guidelines for all relevant stakeholders to improve the state of motorcycle safety in the country.