Many higher secondary schools/colleges from all over Pakistan are affiliated with Aga Khan University Examination Board.

Students qualifying from Aga Khan University Examination Board have secured admissions to the following prestigious institutions:

 Sindh

• St. Joseph's College
• Government D.J. Science College
• P.E.C.H.S College
• Government Delhi College
• Government College for Commerce & Economics
• Government Home Economics College
• DHA College
• PAF College
• Bahria College - Karsaz/Gulshan
• St. Patrick's College
• St. Lawrence College
• Aga Khan Higher Secondary School - Karimabad
• Government National College
• Government P.E.C.H.S. Foundation College
• Government Premier College
• CBM College
• Khatoon-e-Pakistan College
• Government Islamia Science College
• Sir Syed Government Girls College
• Government Abdullah College
• Aisha Bawany College
• Government Shipowners College
• Jinnah College, Nazimabad
• Government Gulshan College
• Government Siraj-ud-Daula College
• Hamdard College
• Fatimiyah Girls College
• Commecs Institute
• APWA Government Girls College
• Government Science & Commerce College F.B. Area
• Government College for Men, Nazimabad
• Government Jamia Millia College
• Government College, Korangi
• Tabani's College
• NCR College
• IISAR Foundation
• St. Bonaventure's High School - Hyderabad
• Mari Gas Higher Secondary School - Dharki

Punjab

• Government College University - Lahore
• Forman Christian College - FC College Lahore
• Lahore Grammar College
• UCL College - Lahore
• Sanjan Nagar Public Education Trust High School - Lahore
• St. Mary's Academy - Rawalpindi
• Mianwali Educational Trust - MET
• Myers Institute of Technology - Chakwal

Northern Areas

• Aga Khan Higher Secondary School (AKHSS) - Gilgit

Others

• Iqra Academy - Abbottabad
• Pakistan Cadet School & College - Murree