Longlines bearing “hook timers” (HTs) and alternating circle (15/0 and 17/0) and “J” (10/0) hooks were employed off the coast of Brazil to measure differences in fishing mortality associated with hook type and on-hook time between capture and boarding. A total of 431 HTs were activated, revealing a clear pattern of the increased mortality rate of fishes associated with increased on-hook time. Swordfish had high mortality rates, unlike blue sharks, which had low mortality rates regardless of hook type and the location in which the hook was transfixed. The six species of tunas and billfishes examined in this study showed a strong association between hooking location and the animal’s release condition, with reduced mortality associated with individuals hooked externally. Results suggest that knowledge of factors affecting the survival of pelagic fishes caught in longline fisheries may enable the development and adoption of fishing methods to reduce mortality of longline bycatch.