During the first three years in Mercy Kilbeggan, all students engage within the new Junior Cycle. Students partake in various core and choice subjects as well as Well-being and various other learning areas and short courses.
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The subjects offered are:
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Core Subjects
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| Irish | English | Mathematics | Science |
| History | Geography |
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Subject Choice
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| German | Materials Technology Wood | Art |
| Metalwork | Technical Graphics | Music |
| Business Studies | Home Economics | French |
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Additional Learning Areas
Well-being, Physical Education (Including Short Course), SPHE, CSPE, Religion, Computer Studies, Classical Studies
