Background: Left ventricular non-compaction (LVNC) is a rare cardiomyopathy typically involving the left ventricle (LV); however, the right ventricle (RV) can also be affected. This case-control study aimed to assess the morphology and function of LV and RV in children with LVNC. Methods: Sixteen children (13 ± 3 years, six girls) with LVNC were compared with 16 sex- and age-matched controls. LV and RV morphology and function were evaluated in cardiovascular magnetic resonance (CMR) studies. Additionally, LV and RV global radial (GRS), circumferential (GCS), and longitudinal strain (GLS) were assessed using tissue-tracking analysis. Results: Patients with LVNC did not differ from the healthy controls in terms of age, height, weight, and body surface area (BSA). In total, 4/16 subjects with LVNC had mid-wall late gadolinium enhancement (LGE). Compared to the control group, patients with LVNC had higher end-diastolic volume (EDV) indexed for body surface area (BSA), lower ejection fraction (EF), and lower LV strain parameters (all p < 0.05). Children with LVNC also presented with thicker RV apical trabeculation, whereas there were no differences in RV EF and EDV/BSA between the groups. Nevertheless, children with LVNC had impaired RV GRS and GCS (both p < 0.05). Conclusions: LVNC in pediatric patients is associated with LV enlargement and impaired LV systolic function. Additionally, children with LVNC have increased RV trabeculations and subclinical impairment of RV myocardial deformation.