Irish, English, Mathematics,CSPE and Science are normally core exam subjects for the Junior Certificate in Boherbue Comprehensive School. In addition, students choose four other exam subjects from the 'option' lines - this refers to the combinations of subjects available on the time table at specific times. These combinations are arranged so that students can have best choice. The option subjects include the following:
- History
- Geography
- Art
- French
- German
- Business Studies
- Home Economics
- Technical Graphics
- Woodwork
- Metalwork
The non exam subjects are:
- SPHE
- PE
- Religion
- Library classes
Having completed the Junior Certificate Students can then opt for Transition Year or the Leaving Certificate.