He was India captain Rohit Sharma's opening partner in the home T20 series against Afghanistan earlier this year but his place looked under threat as he struggled for runs in the IPL
The post has been vacant since Shashank Manohar resigned earlier this month to take over as the chairman of the International Cricket Council. Under new rules, ICC chairman must be an independent administrator with no link to home board.
Thakur, a 41-year-old parliamentarian representing India's ruling Bharatiya Janata Party, was BCCI Honorary Secretary before his elevation, which came at a special general meeting in Mumbai.
BCCI confirmed Thakur's election on their Twitter feed but were yet to name a new Honorary Secretary.