This study assessed the implementation and effectiveness of rape case intervention programs in Boac, Marinduque using an explanatory sequential mixed-method design. A total of 40 respondents—10 Women and Children Protection Desk (WCPD) personnel, 10 Municipal Social Welfare and Development Office (MSWDO) staff, and 20 Barangay Violence Against Women (VAW) Desk Officers—participated in the quantitative phase, which utilized descriptive statistics and the Kruskal–Wallis test. Results showed that the programs were Moderately Implemented and Moderately Effective, indicating partial achievement of program objectives. While basic services were available, deficiencies in funding, facilities, and training limited overall effectiveness. No significant differences were found in perceptions among the three respondent groups (p > 0.05), suggesting common operational challenges across agencies. Qualitative findings highlighted institutional constraints, cultural barriers, and weak inter-agency coordination as major impediments to effective implementation. Insufficient resources, limited technical capacity, and inconsistent training—particularly at the barangay level—were compounded by cultural norms such as hiya, utang na loob, and delicadeza, which discourage reporting and perpetuate victim silence. Despite the presence of legal frameworks such as RA 8353 and RA 9262, program effectiveness remains constrained by socio-economic and institutional limitations, underscoring the need for stronger coordination, sustained capacity-building, and intensified community education to promote survivor-centered and gender-sensitive justice.