Initially, when Sindh was part of the Bombay Presidency, its educational affairs were governed by Bombay University. However, in June 1947, the Sindh University Act was passed, leading to the establishment of Sindh University in Karachi. This university assumed control over both Secondary and Higher Secondary Education in Sindh, previously managed by Bombay University.

In the early post-independence years, Karachi served as the capital of both Pakistan and the Sindh province. However, the provincial government was later relocated to Hyderabad, and plans were made to establish a separate university for Karachi. As a result, Sindh University shifted its operations to Hyderabad. In 1950, the central legislature passed an act establishing the University of Karachi, tasked with overseeing college-level education.

That same year, through the Karachi Secondary Education Act (Act No. XVI of 1950), the Board of Secondary Education Karachi was formed to regulate education from Class 6 to Class 10.

Following the recommendations of the 1956 Commission on National Education (commonly known as the Sharif Commission Report), the education system was divided into Higher Secondary (Intermediate) and Degree Education.

On 8 January 1962, the West Pakistan Government issued the West Pakistan Board of Intermediate and Secondary Education Karachi Ordinance (Ordinance No. III of 1962). This ordinance transferred the authority of Higher Secondary Education from the University of Karachi to the newly created board. The title President of the Board was also replaced with Chairman. Professor Qaiser Hussain Khan Bakhtiari, then President of the Board of Secondary Education, was appointed as the first Chairman of the new Board of Intermediate and Secondary Education Karachi. He officially assumed responsibilities from Dr. Ishtiaq Hussain Qureshi, Vice Chancellor of the University of Karachi, on 2nd November 1961.

The newly established Board conducted its first Higher Secondary Certificate (HSC) examination in May 1962, with around 8,000 candidates and just two affiliated intermediate colleges.

On 19 April 1972, the Government of Sindh introduced the Sindh Board of Intermediate and Secondary Education Ordinance No. VI of 1972, which proposed the bifurcation of the existing board into two separate entities:

Board of Intermediate & Secondary Education, Saddar

Board of Intermediate & Secondary Education, Nazimabad

This ordinance was later amended through the Amendment Acts No. 20 of 1973 and No. 10 of 1974, which led to the formal division of the Board into:

Board of Secondary Education Karachi

Board of Intermediate Education Karachi

Thus, the Board of Intermediate Education Karachi (BIEK) was officially established on 1st February 1974. While the Board of Secondary Education remained in its original premises, the BIEK was set up in the hostel building of the Bakhtiari Youth Centre.

Operating independently since then, the Board conducted its first HSC examination in 1974, with 51,000 students and 50 affiliated colleges. By 2023, the number of examinees had grown to over 275,000, with approximately 409 affiliated colleges under its jurisdiction.