Protein intake of >0.24 g/kg of body weight (BW) at a single meal is necessary to maximize muscle protein synthesis in a young population. However, the association between the protein intake rate for three meals and muscle mass in the young population has not been evaluated. We hypothesized that a protein intake of >0.24 g/kg BW at all three meals is effective for maintaining muscle mass. Therefore, we cross-sectionally examined the association between protein intake at all three meals with muscle mass in 266 healthy young subjects (aged 21.4 ± 2.4 years). Subjects were divided into the AP group, which achieved protein intake >0.24 g/kg BW at all three meals; and the NP group, which did not. We calculated total fat-free mass (FFM) and appendicular fat-free mass (AppFFM) with dual-energy X-ray absorptiometry, and the percentage of total FFM (TotalFFM%) and appendicular FFM (AppFFM%) were calculated as the percentage of BW (%BW). We demonstrated that TotalFFM% (77.0 ± 0.5 vs. 75.2 ± 0.4%, p = 0.008) and AppFFM% (34.7 ± 0.3 vs. 34.1 ± 0.2%, p = 0.058) were higher in the AP than in the NP group. This finding suggests that achieving protein intake of >0.24 g/kg BW at all three meals is important for muscle mass maintenance in young populations.