In March 1996, the 1st joint Bhutan Board-Indian Certificate of Secondary Education Examination (BB-ICSE) was held. From 1996-2000, question papers for Dzongkha, History & Civics, Geography and Economics were set and evaluated in Bhutan and the remaining subjects such as English, Mathematics, Sciences, Computer Science and Commerce were set and evaluated by the CISCE. The ILCS Class XII examination has also been conducted by the BBE since 1996.

November 1999, the conduct and evaluation of the PSCE was decentralized to schools, with the BBE providing the question papers, model answers and marking schemes.

Bhutan Certificate of Secondary Education (BCSE) examination was localized and the BBE took over the conduct of the Class X examination completely. This examination was rescheduled and brought forward from March 2000 to December 1999.

BBE started to coordinate the National Education Assessment (NEA) of student learning and performance using standardized tests and questionnaires

The first NEA on Class VI Literacy (English) and Numeracy (Mathematics) was completed in 2004.

In 2006, the BBE took over the complete conduct of the Class XII examination, called Bhutan Higher Secondary Education Certificate Examination (BHSEC). The first NEA on Class VI Dzongkha was completed in 2006.

From 2007, the BBE started conducting BCSE (Class X) and BHSEC (Class XII) examinations for Continuing Education (CE) candidates. The NEA for Class X Mathematics and English was completed in 2007.

Starting in 2009, the Lower Secondary School Certificate Examination (LSSCE) for Class VIII was fully decentralized to schools. The ILCS Classes X and XII examinations were named as Language and Cultural Studies Certificate Examination (LCSCE). BBE started to conduct the LCSCE (Classes X and XII) for Dzongkha Language Institute (DLI), Thimphu.

From 2011, under Charter 7 of the Accelerating Bhutan’s Socio-economic Development (ABSD) project, the BBE developed and implemented modular Competency Based Assessment (CBA) instruments for Classes V, VII and IX in English, Dzongkha and Mathematics. The second round of the NEA for Class VI Literacy and Numeracy was conducted in 2011 and the report published and disseminated in 2012. The BBE also developed and administered the end-of-year CBA instruments for Classes III, VI and X in English, Dzongkha and Mathematics in 2011. BBE Board meeting was held on August 10, 2011 after having been granted the autonomous status as the Bhutan Council for School Examinations and Assessment (BCSEA) in July 2011.

The development of CBA for Science Class V and History/Civics Classes VII and IX started in 2012 for implementation in 2013. The CBA instruments for Class III Environmental Studies (EVS) were developed and administered in 2012.