This work examined the effects of Secondary Educational Improvement Project (SEIP) on educational outcomes in three (3) Senior High Schools in the Brong Ahafo region. Specifically, the work examined the effects of SEIP on enrolment, its influence with regards to academic performance, the challenges facing its implementation and factors essential to its effective implementation. Using a sequential explanatory approach, primary data was collected in two phases using semi-structured questionnaire and interview guide. Simple random sampling was resorted to in the selection of the three schools. Purposive sampling was used to select 143 beneficiary students, 3 SEIP Coordinators, 1 District SEIP Coordinator and 42 qualified teachers. In all, 189 respondents were sampled. The analysis was done using econometrics techniques to establish the effects of the SEIP programme on educational outcomes. The work revealed that the SEIP policy does not have a significant effect on both academic performance and enrolment. The work revealed the lack of means for verifying the authenticity of socio-economic background of beneficiaries and lack of a proper accountability system.