Exposure to polychlorinated biphenyls (PCBs) has been linked to dyslipidemia. Under acute exposure to PCBs, it has been observed that the secretion of bile acids (BAs) can be impacted, limiting (indirectly) lipid absorption in the gut. In this context, two non-targeted metabolomics studies on pig serum have recently suggested that BA concentrations may fluctuate under exposure to current non-dioxin-like (NDL)-PCB levels in food, reflecting the acute effects of such chronic exposure. The objective of this research is to implement a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for BA analysis in order to validate the findings of previous metabolomics studies, in which BA levels in serum samples from pigs exposed to environmental doses of NDL-PCBs were highlighted to be affected. The proposed LC-MS method involves the use of a C18-pentafluorophenyl LC column, which is not usually selected for the separation of BAs, but shows better performance for the separation of isomers than typical C18 columns. This LC-MS method shows excellent analytical performance such as low limits of detection (LODs) (≤1 ng/mL for most BAs) and good linearity (R2 > 0.994), while no matrix effect was observed. A total of 13 BAs have been quantified, while further BA isomers could be detected and semi-quantified. The application of this targeted LC-MS method confirmed previous findings, suggesting that exposure to low doses of NDL-PCBs decreases the concentration of BAs (i.e., glycochenodeoxycholic acid, hyodeoxycholic acid and taurochenodeoxycholic acid) while the effect on the precursors (cholic acid and chenodeoxycholic acid) is less pronounced.