In this study, eggs from free-range and barn chickens in farms around a fluorochemical facility were collected to assess the distribution profiles of perfluoroalkyl acids (PFAAs), including isomers of perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), and perfluorohexane sulfonate (PFHxS), in egg yolk and albumen. The results revealed that the concentrations of PFAAs in yolks were significantly higher than those in albumen. All 17 PFAAs examined could be detected in yolks, showing decreasing concentrations with increasing distance from the fluorochemical facility. The three predominant compounds in yolks were perfluorobutanoic acid (PFBA, mean concentration 81.4 ng/g ww), PFOS (28.0 ng/g ww), and PFOA (4.83 ng/g ww), and this result is consistent with the product structure of the facility. Moreover, n-PFOA, n-PFOS, and n-PFHxS were the dominant contaminants in yolk, with mean concentrations of 4.75, 25.7, and 4.29 ng/g ww, respectively. In albumen, PFBA was still the predominant PFAA congener (mean concentration = 3.93 ng/g ww), followed by PFOA. Docking analysis indicated that the PFAAs presented higher binding abilities with the low density lipoprotein, high density lipoprotein, and vitellin proteins in yolk than that with ovalbumin albumen proteins, which might be the main factor influencing the possible difference in distributions of PFAAs in yolk and albumen.