Rajnath Singh and incumbent Nitin Gadkari arrived at the party office in the same car for a meeting of the party's parliamentary board, after which he filed his nomination.
Earlier, Rajnath Singh met party leader L.K. Advani.
Rajnath Singh was chosen for the BJP president's post after several senior leaders objected over giving a second term to Gadkari, who is facing corruption charges.
Gadkari also made an announcement Tuesday evening saying he will not seek a second term as he wanted his name cleared of the corruption charges.
The BJP president has traditionally been elected unopposed.
Rajnath's Singh's name emerged after a series of meetings involving party leaders Arun Jaitley, Venkaiah Naidu, Ram Lal and Ananth Kumar.