Background: Primary heart tumors (PHTs) in the pediatric population are very rare and do not manifest any characteristic symptoms. Methods: A retrospective analysis of 61 cases was undertaken. Data from three centers for the years 2003–2018 were gathered. The tumors’ clinical course, location, number, hemodynamic, treatment, and follow-up were evaluated. Echocardiography was complemented with magnetic resonance imaging, computer tomography, and histopathological examination. Results: Out of 61 PHT diagnoses, 56 (91.8%) were circumstantial including all 16 (26.2%) prenatal tumors. The reasons for cardiological consultations were arrhythmia, syncopes, lowered physical performance, and murmurs. Only five patients (8.2%) were suspected of tumors based on previous symptoms of sclerosis tuberosa. Rhabdomyoma was the most frequently found PHT (60.7%). The tumors were predominantly located in the ventricles (49.1%) and intraventricular septum (14.9%) and tended to be single (70.5%). About 37.7% of patients suffered from coexistent multi-organ problems, two (3.28%) from congenital heart defects and one (1.64%) from Carney’s syndrome. Tumor resection was performed on 26 (42.7%) patients, of which 16 (61.5%) underwent total and 10 (38.5%) partial tumor resection. During the follow-up (mean 4.3 years), 54 patients (88.5%) have improved or were stable, while seven (11.5%) died. Conclusions: Primary pediatric heart tumors are diagnosed completely circumstantially, and the most common is rhabdomyoma, although arrhythmia may suggest fibroma. Diagnosis of a heart tumor in children is not synonymous with fatal prognosis, and most of them require only constant observation. Life-saving operation allows improvement, while the prognosis for malignant tumors in children is definitely unfavorable.