Over 9,000 Pradesh Congress Committee delegates were eligible to cast their vote in the election. Both Kharge and Tharoor campaigned ahead of the polls and Congress will get a leader outside the Nehru-Gandhi family as president after 24 years.
The new party chief will have his task cut out with assembly elections having already been declared in Himachal Pradesh and poised to be held in Gujarat.
The presidential election has taken place at the culmination of the party's organisational elections and has come at a time Congress faces multiple challenges.
Congress interim chief Sonia Gandhi was among those who cast their ballot.
"I have been waiting for a long time," Sonia Gandhi had said when media persons asked her on the poll. Sonia Gandhi cast her vote at the All India Congress Committee (AICC) headquarters.
Congress general secretary Priyanka Gandhi Vadra accompanied her mother Sonia Gandhi and cast her vote.
The results will be declared on October 19.
(with inputs from ANI)