This study investigated innovative funding and sustainability of secondary schools in Cross River State, Nigeria. Specifically, it examined the relationship between strategic fundraising programs, collaboration with non-governmental organizations (NGOs), and sustainability of secondary schools. Two null hypotheses were formulated to guide the study. The study adopted a correlational research design, with a population consisting of all 297 principals in public secondary schools in Cross River State. A census sampling method was employed, involving all 297 principals. Data collection was conducted using a researcher-designed questionnaire titled “Innovative Funding and Sustainability of Public Secondary Schools Questionnaire (IFSPSSQ).” The instrument was structured on a four-point Likert scale: Strongly Agree (SA), Agree (A), Disagree (D), and Strongly Disagree (SD). The validity of the questionnaire was established by three experts from the Departments of Educational Management and Educational Foundations (Measurement and Evaluation Unit) at the University of Calabar. The reliability of the instrument was determined using the Cronbach alpha method, yielding coefficient values of 0.78 and 0.84, respectively. Data analysis was performed using Pearson Product-Moment Correlation with the aid of the Statistical Package for Social Sciences (SPSS), version 26. The results revealed a statistically significant relationship between strategic fundraising programs, collaboration with NGOs, and sustainability of secondary schools in Cross River State. Based on the findings, the study concluded that innovative funding has a statistically significant relationship with sustainability of secondary schools in Cross River State, Nigeria. This study contributes to knowledge by emphasizing the role of innovative financial practices in addressing funding gaps, enhancing resources, and supporting educational infrastructure. The findings offer valuable insights for policymakers, administrators, and stakeholders on achieving long-term educational sustainability, particularly in developing regions. Among the recommendations, it was suggested that school principals actively seek collaborations with NGOs to establish partnerships that can provide additional resources and expertise for implementing innovative educational programs and enhancing school infrastructure.