Background: No previous study has defined the prevalence of cardiac geometric and mechanical function abnormalities through the analysis of advanced echocardiographic parameters in children with autosomal recessive polycystic kidney disease (ARPKD). Aim: The purpose of this study was to evaluate cardiac geometry and function through advanced echocardiography in a well-characterized sample of pediatric patients with ARPKD. Methods: Standard echocardiograms were obtained in 27 children with ARPKD (0–18 years) and in 88 healthy children of similar age, gender distribution, and body build. Left ventricular (LV) hypertrophy was defined as LV mass > 45g/(m2.16 + 0.09) and cardiac remodeling was defined by age-adjusted relative wall thickness (RWT). Systolic function was assessed by ejection fraction, midwall fractional shortening (mFS), and global longitudinal (GLS) and circumferential strain (GCS). Results: Patients with ARPKD exhibited a higher LV mass index as compared to controls, and a more concentric LV geometry (both p < 0.001). Accordingly, the prevalence of abnormal LV geometry was significantly higher in ARPKD (33 vs. 0%; p < 0.005). No differences could be observed in the two groups for ejection fraction or GLS (both p = n.s.), while a significantly lower mFS (p < 0.05) as well as GCS (p < 0.001) could be observed. In the analysis of covariance, both LV mass index and RWT remained significantly higher in the ARPKD group, while mFS and GCS remained significantly lower (all p < 0.05). The prevalence of subclinical systolic dysfunction was significantly higher in patients with ARPKD as compared with control subjects (33 vs. 0%; p < 0.001). Conclusions: Children with ARPKD show significantly impaired cardiac phenotype, characterized by high rates of LV abnormal geometry paired with systolic mechanical dysfunction.