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Chlorinated paraffins (CPs) are an emerging and ubiquitous group of environmental pollutants associated with adverse effects on human health, including endocrine disruption and possible carcinogenicity. In this study, supercritical fluid chromatography (SFC) and ultrahigh-performance liquid chromatography (UHPLC) — both coupled with high-resolution mass spectrometry (HRMS) — methods for the analysis of short-, medium-, and long-chain CPs in fish oil-based dietary supplements were developed and validated at concentration levels of 0.6 and 3.0 µg/g lipid weight (lw). The recoveries were in the range of 80–96% and repeatabilities, expressed as relative standard deviations, were <19%. The limits of detection for the UHPLC–HRMS method (from 0.03 to 0.05 µg/g lw) were 5 to 10 times lower than those obtained by SFC–HRMS (from 0.13 to 0.50 µg/lw).