Background: In Hong Kong, the time limitation set for physical education (PE) lessons at schools is one of the obstacles in promoting adequate physical activity (PA) levels for students. Flipped learning is a pedagogical approach that advocate more interaction between teachers and learners, in return promoting more PA participation. The present study utilised the self-determination theory (SDT) as the theoretical framework for designing flipped learning content to be applied during PE lessons, targeting the improvement of students’ PA levels. The purpose of this study was to examine the effectiveness of the flipped learning unit on the PA levels and motivation of students during PE lesson.Method: For this study, 111 Grade 5 students at a Hong Kong primary school participated in the study. They were grouped into a flipped learning group (PE lesson with flipped learning; n=57) or a traditional learning group (PE lesson with regular teaching; n=54). Participants were randomly assigned to groups followed the class they were in. The flipped learning design included an online self-learning session and an in-school learning session with more practice and discussion time allowed during the course of a four-lesson PE learning unit. The lessons for both groups were conducted in twice weekly sessions that lasted for 25 minutes each. An accelerometer (GT3X) was used to measure the PA levels of students during the four experimental PE lessons; and questionnaires were used to assess their motivation before each PE class.Results: Using ANOVA, a significant difference in PA level was found between the traditional learning group and flipped learning group (F, [1,21] = 21.76, p < .05). Moderate to vigorous physical activity (MVPA) duration of the flipped lessons was higher and duration of sedentary (SED) was lower than that of the traditional lessons. At the same time, autonomous motivation was a positive predictor of MVPA (β = 1.603, p < 0.05) in practice-oriented lessons. In addition