The current level of annual incidental bycatch of gray seals Halichoerus grypus in the New England sink gillnet fishery is the highest for all marine mammal species in the USA. One way to evaluate the risk of bycatch is to examine the risk of encounter between an animal and fishing gear based on the animal’s habitat use in relation to fishing activity. Here we used satellite telemetry deployed on 30 gray seal pups in 2019 and 2020 to measure the risk of encounter with large-mesh sink gillnet fishing effort throughout the Gulf of Maine and southern New England. We estimated relative encounter risk within 30 min grid cells in each calendar quarter based on the overlap of seal presence and fishing effort, and then validated the expected risk based on bycatch events reported by independent observers on board fishing vessels. The relative risk of seals encountering gillnet fishing gear was highest off southeastern Massachusetts in spring. Patterns in the estimated encounter risk fit our expectation that relatively high levels of habitat use and fishing effort correspond to increased encounter risk. The approach taken here can be used to identify times and areas of high encounter risk to justify altered fishing practices for purposes of avoidance, or to target observer monitoring intended to characterize and quantify bycatch. Mitigation strategies will need to be continuously monitored and updated to incorporate new information as conflicts with fisheries and gray seals are likely to continue.