This study aimed to test an observational momentary time sampling tool to estimate in-class moderate-to-vigorous physical activity (MVPA), in terms of validity, reliability and agreement between observational momentary time sampling and accelerometry, and to develop a regression equation to estimate MVPA from observational momentary time sampling. The sample comprised 78 pupils (38 girls), mean age 14.0 ± 1.1 years. Measurements were taken in three similar Physical Education classes, on three different days. To monitor MVPA, we applied the observational momentary time sampling method. Students wore an ActiGraph GT3X+ accelerometer. Reliabilities were determined by the intraclass correlations, the agreement between methods was analyzed using the Bland–Altman method, and a multiple regression analysis was performed to estimate the equation. The observational momentary time sampling showed good reliability across time (0.59 < r < 0.72, p < 0.001). It was significantly correlated with accelerometry (r = 0.51, p < 0.001). The MVPA assessed via accelerometer could be predicted from the following equation: Y = 44.3 + 0.47⋅(MVPA observational momentary time sampling method) + 8.0⋅(sex; with 0 = girls and 1 = boys). This observational momentary time sampling method is a stable and reliable tool to estimate MVPA. A regression equation using the score of observational momentary time sampling and sex can be used to better estimate the real MVPA.