In search of an accurate and effective method to determine fatty acid composition in silkworm pupae oils, five methylation methods were evaluated for use in the gas chromatographic (GC) quantitation of fatty acid methyl esters (FAMEs), including one-step esterification catalyzed by an acidic (H2SO4 and BF3) or alkali catalyst (KOH and NaOCH3) and a two-step procedure catalyzed successively by KOH and H2SO4. These methods were comparatively adopted to quantify FAMEs in silkworm pupae oil using GC-MS and GC and then validate their precision, stability and average recovery rates. The results indicated that compared with the other four methyl esterification methods, two-step methylation effectively improves the synthesis yield of FAMEs, conserves agents, and eliminates the usage of potential harmful reagents. The proposed GC method has been validated, shows good accuracy and precision, and has been applied successfully to the quantification of FAMEs in several varieties of silkworm pupae oils. The short analytical run time leads to low costs and a fast chromatographic procedure. In summary, two-step pretreatment had superior performance, providing technical references for the determination and analysis of fatty acids in other oils.