The concentration of human milk oligosaccharides has gained significant attention recently due to their positive effects on infant health. However, the concentration of 3-fucosyllactose(3-FL) in Korean mother milk has not been studied. Therefore, this study aimed to analyze the concentration of 3-FL in Korean human milk using mass spectrometry. The analytical method for quantitating 3-FL was validated to have high precision, accuracy, linearity, specificity, stability, recovery, and reproducibility. The concentration of 3-FL was then determined in 102 Korean human milk samples. The results showed that the 3-FL concentration increased during lactation, with values of 1.0, 1.1, and 1.8 g/L in 0–30, 30–60, and > 60 postpartum days, respectively. Notably, the 3-FL level in secretors (1.3 g/L, n = 80) was significantly lower than in non-secretors (2.8 g/L, n = 24). These findings provide useful information for future research, as well as for setting the recommended nutrient intake (RNI) value and formulating baby food composition.