Background: Schools are increasingly experiencing physical, psychological, and sexual violence, which impacts students’ academic achievement and physical and emotional health. Our objective was to identify regional prevalence rates, average prevalence by aggressor type, and provincial spatial conglomerates with higher rates for each type of school violence reported in educational settings in Peru during 2019. Methods: An analysis was made of 12,132 cases reported through Peru’s Specialized School Violence System (SíseVe). The Moran indices were calculated using provincial prevalence rates to identify conglomerates with high prevalence. Results: In the coast region, the Department of Tacna reported the highest prevalence rates for physical (99.7) and psychological (107); the Department of Amazonas, which is in the jungle, reported the highest prevalence rate for sexual violence (74.6), with teachers in public schools accounting for the majority of sexual assaults against students (56%). Conclusions: Sexual violence predominated in the jungle zone, with a significant percentage of teachers participating in violence with sexual connotations. Physical and psychological violence prevailed in the coastal region.