Perfluorinated compounds (PFCs) are ubiquitous in the environment and are becoming a public health concern. It is desirable to develop sensitive and accurate methods to measure PFCs in non-invasive matrices such as hair and nail for biomonitoring of body burden. Different extraction methods coupled with solid phase extraction were investigated for extraction efficiency. The extracts were separated, identified and quantified by liquid chromatography-tandem mass spectrometry. Extraction with acetonitrile proved to be the most efficient extraction method for human hair sample, while extraction by methanol with alkaline digestion performed best for human nail sample. The matrix recoveries of the optimized methods ranged from 78% to 116% for hair and from 87% to 126% for nail sample. The ranges of the limit of detection (LOD) were 0.026–0.069ng/g and 0.023–0.094ng/g for hair and nail, respectively. These methods were validated by evaluating LOD, accuracy and precision and were proven to be useful for measuring paired human hair and nail samples collected from the general population.