The objective of this study was to determine diagnostic accuracy of magnetic resonance imaging (MRI) and computed tomography (CT) scans in young athletes diagnosed with spondylolysis. A cross-sectional study was used. Twenty-two young athletes (14.7 ± 1.5 years) were diagnosed as spondylolysis based on a single-photon emission CT. Following the diagnosis, participants underwent MRI and CT scan imaging tests on the same day. The sensitivity and false-negative rate of the MRI and CT scans were analyzed. MRI test confirmed 13 (+) and 9 (−) results while CT test showed 17 (+) and 5 (−) results. The sensitivity and false-negative rate of MRI were, respectively, 59.1% (95% confidence interval [CI] = 36.7% to 78.5%) and 40.9% (95% CI = 21.5% to 63.3%). Furthermore, the sensitivity and false-negative rate of CT scan were 77.3% (95% CI = 54.2% to 91.3%) and 22.7% (95% CI = 0.09% to 45.8%). Our results indicated that CT scan is a more accurate imaging modality to diagnose spondylolysis compared with MRI in young athletes.