Pupils are organised into classes which are part of a year group as follows:
| Malvern College Egypt Class | Age at 1st October |
| Pre-Nursery | 2 Years 6 Months |
| Nursery | 3 Years 6 Months |
| Reception | 4 Years 6 Months |
| Year 1 | 5 Years 6 Months |
| Year 2 | 6 Years 6 Months |
| Year 3 | 7 Years 6 Months |
| Year 4 | 8 Years 6 Months |
| Year 5 | 9 Years 6 Months |
| Year 6 | 10 Years 6 Months |
| Year 7 | 11 Years 6 Months |
| Year 8 | 12 Years 6 Months |
| Year 9 | 13 Years 6 Months |
| Year 10 | 14 Years 6 Months |
| Year 11 | 15 Years 6 Months |
| Year 12 | 16 Years 6 Months |
| Year 13 | 17 Years 6 Months |
As with Malvern College UK and most other British International Schools around the world, Malvern College Egypt also offers a system whereby pupils are able to graduate at the end of Year 13. In this pathway, pupils will complete (I)GCSE qualifications by the end of Year 11. Pupils will then move into the Sixth Form programme to study for their final two years A-Levels or IBDP.
Either of these programmes will give pupils the opportunity to achieve grades and the required number of qualifications to study at any University around the world in most cases this would not require the study of the Foundation Year course prior to the Degree.
Malvern College Egypt offers pupils the opportunity to graduate from Secondary School at the end of Year 12. For some pupils, who have not studied in other countries or are age appropriate to complete their studies at the end of Year 12, this will allow for application to universities throughout Egypt or onto Foundation Year courses and subsequent degrees at other universities around the world. Any pupil wishing to take this pathway will be required to take the full complement of IGCSE examinations at the end of Year 10. They will then be able to take tailored A-Level Programme or IBDP Programme.