In order for a school to become affiliated with the Aga Khan University Examination Board, the institution must follow a series application, review and approval procedures as set by the AKU-EB Board of Directors. Affiliation will be renewed annually, subject to compliance with the procedures set forward by AKU-EB; affiliated schools can and will be subject to visits and reviews that ensure this compliance.

There are several categories of affiliation that can be awarded to schools, depending on AKU-EB's evaluation of the school's capabilities in meeting the requirements for both preparing candidates for AKU-EB examinations and potentially even conducting AKU-EB examinations themselves.

Schools will be evaluated according to a number of criteria that AKU-EB's Quality Assurance team must be satisfied are being fulfilled. For example, the physical premises of the school should be sufficiently clean, have due safety procedures for both students and staff, provide necessary spaces such as science laboratories and libraries (which must also be properly equipped according to AKU-EB specifications), and should also have audio equipment capable of sufficient amplification for classroom use.

Staff at affiliated schools must have relevant qualifications in the subjects that they teach. All teachers engaged in the teaching of AKU-EB syllabi must have a copy of the relevant subject syllabus and, if required, should receive training that will be provided by AKU-EB. Schools should also be prepared to provide all reasonable access to teaching space, students and teachers to authorized representatives of AKU-EB.

Investigations by AKU-EB, as prompted by suspicious circumstances either being reported by the school itself or AKU-EB's internal quality control procedure, must be complied with fully.