Quantification of left ventricular (LV) mass by echocardiography has not been validated against the gold standard of cardiac magnetic resonance imaging (CMR) in the pediatric population. The purpose of this study was to compare LV mass by two-dimensional and conventional M-mode echocardiography versus CMR in children. Consecutive CMR studies were paired with echocardiograms and retrospectively analyzed in children age ≤ 16 years (3 days old to 16 years old). Studies performed > 3 months between modalities and single ventricle anatomy were excluded. Unindexed LV mass was calculated using M-mode, area-length (AL), and truncated ellipsoid (TE) methods via echocardiography, and compared to cine stack CMR images. There were 46 patients included in the study (both MRI and echocardiography). Good correlations were observed for LV mass measured by CMR and all echocardiographic methods: M-mode (R = 0.965), AL (R = 0.975), and TE (R = 0.975). There was a significant overestimation using TE echocardiography, by a mean of 10.5 g (95% confidence interval 5.7–15.2 g, p < 0.05). There was no significant over- or underestimation of LV mass observed by M-mode or AL echocardiographic measurements, with tight limits of agreement when compared to CMR (95% confidence interval − 5.2 to 4.4 g and − 1.5 to 6.7 g, respectively). Interobserver agreement was good for each of the echocardiographic measurements, but inferior with M-mode (ICC, 0.89) compared to two-dimensional methods (ICC, 0.97). Echocardiographic estimates of LV mass have good correlation with CMR in children. Performance comparison showed AL echocardiographic method provides the most accurate measurement of LV mass with the best reproducibility compared to other methods.