The study was designed to explore the integration of GEQIP programs with operations of schools focus on structural integration and role clarity in primary schools in aysaita woreda . with specific objective of the study being; to investigate the actors role clarity in implementing GEQIP programs, integration among GEQIP programs , integration of GEQIP programs with the regular functions of schools. The study was carried out at three primary schools in aysaita woreda and was conducted using case study design. The study used qualitative methods of data collection. It also used the purposive sampling designs in the identified schools were purposively sampled. The schools were sampled due to their implementation of programs .The study made use of both secondary and primary data. Secondary data was drawn from GEQIP documents schools reports and evaluation documents of WEO. In-depth interviews were used to collect information from principals, vice principals and program coordinators. The data collected was qualitatively analyzed. The study found out that principals, vice principals, program coordinators, department heads in schools were not clear about their role in implementing GEQIP. Actors in the schools operated within their respective programs. Each programs operated independent of each other and lack of integration among programs and between programs and regular functions of school. The study also established that the actors roles duplicated and overlapped each other and programs efforts and regular functions duplicated. The study established that other challenges in the GEQIP implementation included limited awareness of their roles in implementing GEQIP and other actors roles within the sector, inadequate funding for program implementation . The study made recommendations on how to improve the overall implementation of the GEQIP programs in the schools. These recommendations included among others, the need to establish a coordinating post or mechanism that spells out the roles of various actors and linkages, need to work on integration of programs and schools regular functions by running programs by existing structure of schools in order to remove duplication and overlaps as well as need for further research on role clarity and structural integration of GEQIP with operations of school