Pelagic fishes support a vital part of the local and export production and trade at global, regional, and local levels. In the Western Indian Ocean, pelagic fishes are mainly exploited by purse-seiners and long-line fishing vessels operating in national exclusive economic zones and international waters. Catch data from these vessels is often not adequately evaluated to determine the variation of catches and the state of the exploited stocks. This study evaluates the Kenya long line fishery between 2016 and 2020 to determine catch rates, temporal variation over time, and the key species’ maximum sustainable yield (MSY). The catches were dominated by Xiphias gladius (44.7%), Thunnus albacares (24.4%), Thunnus obesus (10.9%), and Prionace glauca (7.7%). Catch rates were significantly different among years, months, vessels, and depths for all species except for X. gladius and P. glauca, whose catch rates did not significantly differ at different depths. The catch rates for X. gladius, T. obesus, and T. albacares were higher during the northeast monsoon season, while P. glauca had higher catch rates during the southeast monsoon season. The maximum sustainable yield (MSY) was higher than the annual catches for the four species. We recommend catch rates be monitored over a more extended period for trend comparison and future work to consider discards encountered during fishing. We recommend seasonal closures for management, especially for the vessels targeting tunas and swordfish to conduct fishing during the NEM season when the catch rates are higher. There is a need for future work to focus on hook selectivity for the long-line fisheries along the Kenya EEZ.