The aim of this study was to evaluate the association between overweight/obesity and future academic performance among high-school students in Saudi Arabia. This was a retrospective cohort study of 257 12th grade female students in Alabna (Ministry of Defence) high schools in Riyadh during 2013/14. Overweight/obesity was based on weight and height at 10th grade. Decline in academic performance was defined as a reduction by > 1 standard deviation in marks between 10th and 12th grades. One hundred and five students were overweight/obese and 30 had declined academic performance. Self-esteem scale was similar in both groups. In a multiple logistic regression model adjusted for sociodemographic characteristics, study-related lifestyle and self-esteem, overweight/obesity was associated with declining academic performance. Other independent associates included paternal and maternal education, and living outside governmentally provided housing. We report a negative independent association between overweight/obesity and subsequent academic performance among female high-school students in Saudi Arabia. The results highlight the need for community and school programmes to target overweight/obesity among high-school students.