Behçet's disease (BD) is a systemic disease with unknown etiopathogenesis and varying disease presentations. Fatty acids (FA) are essential biological compounds that are involved in complex metabolic pathways. They may contribute to inflammation and endothelial dysfunction by participating in many signaling pathways. Increased FAs levels are associated with an increased risk for various diseases. This study aimed to determine the relationship between FA, BD, and thrombotic complications. A total of 97 patients were recruited from the rheumatology department of a single center as a case–control study. The participants were divided into three groups: 36 patients with BD with thrombosis (Group 1), 24 patients with BD without thrombosis (Group 2), and 37 age- and sex-matched controls (Group 3). The analysis of 37 different FA with carbon numbers in the range of (4:0) and (24:1) in the samples were analyzed and compared between groups. Myristic acid (MA), methyl eicosatrienoate, and stearic acid (STA) levels were found to be significantly higher in BD with thrombosis than in BD without thrombosis, and palmitic acid (PA) levels were significantly higher in BD with thrombosis than in healthy individuals. MA was found to be a significant marker for differentiating between thrombotic BD. PA and STA are important markers for detecting thrombotic BD. In BD, lipotoxicity created by FA, such as PA, STA, and MA, plays a role as an inducer of inflammation and thrombosis through various mechanisms.