Greenways are linear open spaces, which are often used as trails for pedestrians and cyclists, but junctions with roads are a safety concern and act as a potential impediment to active transportation. This study evaluated crossing behavior patterns and safety at greenway–road junctions in New Orleans, LA. Crossing behaviors, safety and motor vehicle behavior were collected using direct observation methods. Intercept surveys were conducted to assess greenway use and safety perceptions. Logistic and negative binomial regression were used to assess the relationships between crossing signal (rectangular rapid flash beacon) activation and motor vehicle behavior. Fewer unsafe crossings occurred when the crossing signals were activated for cyclists and pedestrians (p-values of 0.001 and 0.01, respectively). There was no association between pedestrian use of crossing signals and motor vehicle stopping behavior but cyclists had significantly higher odds of motor vehicles failing to stop when the signal was activated (OR 5.12, 95% CI 2.86–9.16). The activation of rectangular rapid flash beacons at urban greenway junctions with roads did not influence motor vehicle behavior. Differences in crossing safety by signal use cannot be attributed to the signal’s influence on motor vehicle stopping behavior.