Lipids in human colostrum provide the majority of energy intake and essential fatty acids for developing infants. The fatty acid composition of human colostrum is highly variable and influenced by multiple factors. Human colostrum is a complex sample bringing challenges to fatty acid profiling. This work aimed to optimize the use of ionic liquid (IL) columns and flow-modulated comprehensive two-dimensional gas chromatography coupled to mass spectrometry (FM-GC×GC-MS) for fatty acid profiling in human colostrum. Derivatization strategies were optimized and the elution behavior of fatty acid methyl esters (FAME) on various 1D column phases (Solgel-WAX, SLB-IL60i, SLB-IL76i, and SLB-IL111i). Derivatization with sodium methoxide yielded a satisfactory recovery rate (90%) at milder conditions and reduced time. The use of IL60 as the 1D column provided superior separation, good peak shape, and better utilization of elution space. As a proof of concept, the developed method was applied to access the effects of the mode of neonatal delivery (vaginal vs. C-section) on the fatty acid profile of human colostrum samples. The integrated multidimensional gas chromatography strategy improved FAME detection and separation and can be a useful tool for accessing the effects of different factors on the fatty acid profiling of complex samples.