Our aim was to assess the validity of the brief-type self-administered diet history questionnaire (BDHQ15y) to estimate the protein intake in 248 Japanese secondary school students (mean age = 14.2 years), using urinary biomarkers as references. Participants provided three samples of overnight urine for measurement of urea nitrogen and creatinine levels, underwent anthropometric measurements, and answered the questionnaires. Additionally, 58 students provided 24-h urine specimens. A significant correlation was observed between excretion of urea nitrogen in overnight and 24-h urine specimens (ρ = 0.527; p < 0.001), with biases ≤5.8%. The mean daily protein intake estimated from urinary biomarkers was 76.4 ± 20.4 g/d in males and 65.4 ± 16.9 g/d in females, and the mean protein intake estimated from the BDHQ15y (PRTbdhq) was 89.3 ± 33.7 g/d in males and 79.6 ± 24.6 g/d in females. Crude and energy-adjusted coefficients of correlation between PRTbdhq and protein intake estimated from urinary biomarkers were 0.205 (p = 0.001; 0.247 for males and 0.124 for females), and 0.204 (p = 0.001; 0.302 for males and 0.109 for females), respectively. The BDHQ15y is a low-cost tool to assess protein intake of a large population, instead of a weakness of overestimation.