One-anastomosis gastric bypass is a promising type of bariatric surgery, but it may lead to a deficiency in important nutrients, such as fatty acids. The short-term effects of one-anastomosis gastric bypass on serum fatty acids have not been studied thus far. Therefore, the aim of this study was to determine the effect of one-anastomosis gastric bypass on serum fatty acid composition two weeks after surgery. This study included 38 patients who underwent one-anastomosis gastric bypass as surgical treatment for morbid obesity. Serum fatty acid composition was analyzed before and two weeks after surgery using gas chromatography-mass spectrometry. We observed a decrease in essential polyunsaturated fatty acids ( < 0.001 for linolenic acid and < 0.001 for linoleic acid) and odd-chain fatty acids ( = 0.004) in the serum of obese patients shortly after a one-anastomosis gastric bypass. Considering the benefits of the aforementioned fatty acids for human health, the implementation of a fatty-acid-rich diet or the use of supplementation may be recommended for patients immediately after one-anastomosis gastric bypass.