Background/Objectives: Pediatric myelodysplastic syndrome (pMDS) is a rare, heterogeneous, clonal hematopoietic stem cell disease with a risk of evolution to acute myeloid leukemia (AML). Clonal cytogenetic abnormalities are present in 30–60% of pMDS. However, unlike in adults, the prognostic significance of chromosomal alterations, particularly their role in predicting evolution to AML, remains limited in pMDS. To acknowledge this gap, we studied the cytogenetic abnormalities in pMDS and analyzed their associations with subtypes and evolution to AML. Furthermore, in the Discussion Section, we pointed out key genes involved in these chromosomal alterations. Methods: Cytogenetic analysis was performed on 193 pediatric patients using G-banding and fluorescence in situ hybridization. Results: Abnormal karyotypes were observed in 43.5% (84/193) of patients, mainly in the advanced subtype. The main chromosomal alterations were monosomy 7 (−7) in 14% of the cases (12/84), deletion of the long arm of chromosome 11 [del(11q)] in 12% (10/84) and both trisomy 8 (+8) and deletion of the long arm of chromosome 7 [del(7q)] in 8% (7/84). Evolution from MDS to AML was observed in 22% of the patients (42/193), and it was associated with complex karyotypes, del(11q), −7/del(7q), and +8. Conclusions: Our results suggest that specific chromosomal alterations, such as del(11q), del(7q), and +8, may predict evolution to AML and might be considered high-risk cytogenetic markers in pMDS.