The primary objective of this longitudinal study was to determine the association between cardiorespiratory fitness and the risk of overweight status in youth. To accomplish this aim we analyzed data from annual school-based surveys of cardiorespiratory fitness and anthropometry conducted between 2004 and 2006. The first analysis was performed on a cohort of 902 youth aged 6–15 years followed for 12 months to assess the association between cardiorespiratory fitness levels determined from a graded maximal field test and the risk of becoming overweight. The second analysis was conducted on a cohort of 222 youth followed for 2 years to assess the continuous association between annual changes fitness and weight gain. Children with low cardiorespiratory fitness were characterized by higher waist circumference and disproportionate weight gain over the 12-month follow-up period (P < 0.05). Within the entire cohort, the 12-month risk of overweight classification was 3.5-fold (95% confidence = 2.0–6.0, P < 0.001) higher in youth with low cardiorespiratory fitness, relative to fit peers. A time series mixed effects regression model revealed that reductions in cardiorespiratory fitness were significantly and independently associated with increasing BMI (r = −0.18, P < 0.05) in youth. Accordingly, low cardiorespiratory fitness and reductions in fitness over time are significantly associated with weight gain and the risk of overweight in children 6–15 years old. An assessment of cardiorespiratory fitness using a common field test may prove useful for the identification of youth at risk of overweight and serve as a potential target for obesity prevention.