The datafile includes nitrogen and carbon isotope analyses of seven baleen plates from six individuals of sei whales (Balaenoptera borealis) from the Chilean-Patagonian fjord area in 0.5 cm resolution. The baleens are from dead carcasses all stranded, except of one, after a mass mortality event in 2016 (Häussermann et al. 2017; https://doi.org/10.7717/peerj.3123 ).Carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope variations in baleen plates of sei whales (Balaenoptera borealis) stranded after a mass mortality event in Chilean Patagonia were analyzed to assess potential dietary and migratory patterns. Carbon and nitrogen isotope ratios of seven baleens from six individuals were analyzed. The δ¹³C values ranged from -19.1 to -15.9 ‰ and the d15N values from 8.7 to 15.4 ‰. Variations of up to 2.9 ‰ for δ¹³C and 5.3 ‰ for δ¹⁵N were observed within one baleen. Carbon and nitrogen isotope records of each baleen were significantly correlated and showed recurring oscillations confirmed by wavelet analyses. Oscillations slightly differed in periodicity indicating variable baleen growth rates between 10.0 and 16.5 cm yr-1. Food sources of the whales are discussed in terms of available isotope data for potential prey taxa and potential migratory behavior on the basis of latitudinal isotope gradients of particulate organic matter. Cyclicity could be explained by regular migrations of the sei whales from subtropical calving areas to high-latitude foraging grounds. δ¹⁵N records of baleens differed between individuals eventually pointing to diverse feeding and migratory preferences among sei whale individuals.