Objective To evaluate the relationship between bus stop characteristics and pedestrian–motor vehicle collisions. Methods This was a matched case–control study where the units of study were pedestrian crossings in Lima, Peru. We performed a random sample of 11 police commissaries in Lima, Peru. Data collection occurred from February 2011 to September 2011. A total of 97 intersection cases representing 1134 collisions and 40 mid-block cases representing 469 collisions that occurred between October 2010 and January 2011, and their matched controls, were included. The main exposures assessed were presence of a bus stop and specific bus stop characteristics. The main outcome measure was occurrence of a pedestrian–motor vehicle collision. Results Intersections with bus stops were three times more likely to have a pedestrian–vehicle collision (OR 3.28, 95% CI 1.53 to 7.03), relative to intersections without bus stops. Formal and informal bus stops were associated with higher odds of a collision at intersections (OR 6.23, 95% CI 1.76 to 22.0 and OR 2.98, 1.37 to 6.49). At mid-block sites, bus stops on a bus-dedicated transit lane were also associated with collision risk (OR 2.36, 95% CI 1.02 to 5.42). All bus stops were located prior to the intersection, contrary to practices in most high-income countries. Conclusions In urban Lima, the presence of a bus stop was associated with a threefold increase in risk of a pedestrian collision. The highly competitive environment among bus companies may provide an economic incentive for risky practices, such as dropping off passengers in the middle of traffic and jockeying for position with other buses. Bus stop placement should be considered to improve pedestrian safety.