Principals of secondary schools play a very important role in enhancing students’ academic achievement. However, in the process of doing this, studies have shown that, principals are faced with a number of challenges resulting in poor performance of students. Public Secondary Schools in Ndhiwa Sub County have not been performing well academically as shown by Kenya Certificate of Secondary Education examination results between the years 2013 and 2018, compared to the neighboring Sub Counties within Homa Bay County. On the other hand, the average Kenya Certificate of Secondary Education mean scores was 4.7 when compared to other Sub-counties, which are higher; Homa-Bay: 6.0; Suba: 5.0 Rachuonyo North: 5.1; Rachuonyo South: 5.2; Mbita: 5.3. Hitherto the school based challenges principals face relating to their areas of operations were unknown in Ndhiwa Sub County, the knowledge gaps this study sought to fill. The objective of this study was to determine school based challenges faced by principals in enhancing students’ academic achievement in Public Secondary Schools in Ndhiwa Sub County, Kenya. Grounded theory was used to guide the study. A conceptual framework based on concept that c school based challenges faced by principals (Independent Variable), must be overcome in order to enhance student academic achievement (Dependent Variable) was used. The study established that school based challenge posed bigger challenge to the principals in enhancing students’ academic achievement as indicated by the overall mean rating of 3.64. The study recommended that: principals need to be given a lot of training on management of finances to enable them manage the financial resources available in their schools; the stakeholders like the Boards of Management should think of other sources of funds that the schools can engage in to boost the financial resources; the principals and teachers should give priority to developing the attitude of students positively to enhance performance of students in their schools.