This study aimed at providing answers to two key questions: 1) Which subjects are most preferred by students in secondary schools? 2) What are the reasons behind the students’ interest, or lack thereof, in particular subjects? The study employed qualitative methodology using a multiple case study holistic design. The students in the studied schools served as the unit of analysis. The study involved a sample of 18 secondary schools that were purposefully selected. Data were collected using focus group discussions, observation and documentary review. The analysis involved the use of the Miles and Huberman’s model of qualitative data analysis. The findings show that the majority of students in secondary schools preferred arts subjects notably because of the challenges they experience in learning science. The reasons for students preference of a particular subject included the inspiration from significant others, commitment and support provided by the subject teachers, the availability of teachers and their teaching approaches and relevance of the subject to their daily life experiences. On the basis of these findings, it is recommended that the government should create a conducive learning environment, especially for community secondary schools, that will allow students to select subjects on the basis of their ability and interests.