Grade 9 pupils’ choice of a course to pursue in senior high school in Ghana is a decision made at a young age usually below 16 years. Therefore, these young pupils rely on other persons for help when making such a decision. Previous research found that instead of assisting, these social agents rather interfere with this decision-making process. This study explored the challenges grade 9 pupils face in choosing courses in their transition to senior high school by seeking the views of the pupils and their teachers/counsellors using a questionnaire and interview guide. The findings showed that fathers, mothers, siblings, finances and orientation at home were the major obstacles the pupils faced when selecting a course to pursue. Other challenges found in the school setting included teacher interferences and peer distractions. The study concluded that grade 9 pupils have a great challenge from their social milieu when choosing a course to pursue at the senior high school level. The study recommended that school counsellors/heads should educate parents, guardians and teachers on how to guide pupils in choosing a course to pursue at the SHS level