We investigated the concentrations of 45 per‐ and polyfluoroalkyl substances (PFASs) in fledgling flesh‐footed shearwater (Ardenna carneipes; n = 33) and wedge‐tailed shearwater (A. pacifica; n = 9) livers via liquid chromatography–tandem mass spectrometry and their relationship to body morphometrics and ingested plastic mass recorded in 2019 on Lord Howe Island (NSW, Australia). Sixteen PFASs were detected, of which perfluorooctanesulfonate (PFOS) was the dominant compound, detected in 100% of birds (1.34–13.4 ng/g wet wt). Long‐chain perfluorocarboxylic acids, including perfluorodecanoic acid (PFDA; <0.04–0.79 ng/g wet wt) and perfluorotridecanoic acid (PFTrDA; <0.05–1.6 ng/g wet wt) were detected in >50% of birds. There was a positive correlation between PFDA and PFTrDA concentrations and wing chord length (Rs = 0.36, p = 0.0204; Rs = 0.44, p = 0.0037, respectively), and between PFDA concentrations and total body mass (Rs = 0.33, p = 0.032), suggesting that these compounds may impact shearwater fledgling morphometrics. Plastic was present in the intestinal tract of 79% of individuals (<7.6 g), although there was no correlation between PFAS concentrations and plastic mass, indicating that ingested plastic is not the likely primary exposure source. The widespread occurrence of PFASs in fledgling marine birds from a relatively pristine location in the Southern Hemisphere suggests that further studies in adult shearwaters and other marine birds are warranted to investigate whether there are any long‐term physiological effects on bird species. Environ Toxicol Chem 2021;40:799–810. © 2020 SETAC Background: Image of Lord Howe Island looking south towards Mount Gower. Map: Location of Lord Howe Island (red star) in relation to Australia and New Zealand. Bird: Artists impression of the Procellariidae family of birds, including the Flesh‐footed Shearwater and the Wedge‐tailed Shearwater. Graph: Sum concentrations of eight classes of PFASs detected in livers from juvenile Wedge‐tailed and Flesh‐footed Shearwaters from Lord Howe Island in 2019. PFAS = per‐ and polyfluoralkyl substances; PFCA = perfluorocarboxylic acids; PFSA = perfluoroalkylsulfonic acids; FTCA = fluorotelomer carboxylic acids; FTSA = fluorotelomer sulfonic acid; PASF = perfluoroalkyl sulfonyl fluoride; PFES = perfluoroalkyl ether sulfonic acid; diPAP = fluorotelomer phosphate diester; PFPiA = sodium bisheptadecafluorooctylphosphinate.