To determine whether health-related physical fitness and body mass index (BMI) status differed before and after school closure from the COVID-19 pandemic in a population-based cohort of Hong Kong primary schoolchildren. We examined the BMI z score, BMI status, and physical fitness z scores including (i) upper limb muscle strength, (ii) 1-minute sit-up test, (iii) sit-and-reach test, and (iv) endurance run tests, among 3 epochs: prepandemic (September 2018-August 2019), before school closure (September 2019-January 2020), and partial school reopening (September 2021-August 2022), using a repeated cross-sectional approach. A total of 137 752 primary schoolchildren aged 6-12 years were recruited over 3 academic years. Obesity increased significantly from 25.9% in 2018/19 to 31.0% in 2021/22, while underweight increased slightly from 6.1% to 6.5%. All tested parameters were adversely affected by the pandemic. The negative trend over time was far more pronounced in all 4 physical fitness scores in the underweight group, although performance in handgrip strength had no significance between 2018/19 and 2021/22. Schoolchildren who are both underweight and overweight/obese are vulnerable to adverse changes in physical fitness during the COVID-19 pandemic. To eliminate the negative health and fitness outcomes, it is urgent to develop strategies for assisting schoolchildren in achieving a healthy weight, especially in the postpandemic era.