Determination of the fatty acid profile in milk samples is one of the most important in food analysis. There are many methodologies for FA determination. The conventional procedure for determining the FA composition of milk is isolation of fat or indirect methylation, trans-methylation, extraction of fatty acids, and analysis by gas chromatography. In this study, eight methods based on alkaline methylation were compared for the analysis of fatty acids in cow’s milk. The response factors (RF) for GC analysis using FID were calculated. For most acids, RFs were close to 1, with the exception of short-chain fatty acids (C4:0–C8:0). To facilitate the selection of the method for the determination of fatty acids in milk samples, the methods were assessed using the environmental assessment tools of the analytical procedure: the Analytical Eco-Scale, Green Analytical Procedure Index (GAPI), and Analytical Greenness for Sample Preparation (AGREEprep). The method based on direct milk methylation received the highest scores. Omitting the lipid separation step has an impact on reducing the quantity of used toxic chemicals and reagents, and produces a smaller amount of waste, a much higher throughput, and a reduced cost analysis.