Jakhar is leading in all nine assembly constituencies.
The counting started at 8 am.
Meanwhile, AAP candidate Maj. Gen. (Retd) Suresh Khajuria accused the Congress of using "undemocratic means" in the bypoll.
"Ruling party used undemocratic means in these elections. People were scared and youth was almost absent in the bypoll. If they (Congress) win then that victory will not be a respectable one," Khajuria alleged.
Two counting centres have been set up for the counting of votes.
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Tight security arrangements have been made at the counting centres, official said.
The Gurdaspur Lok Sabha seat has nine Assembly segments -- Bhoa, Pathankot, Gurdaspur, Dinanagar, Qadian, Fathegarh Churian, Dera Baba Nanak, Sujanpur and Batala
The result will decide the fate of total 11 candidates including Congress nominee Jakhar, BJP's Salaria and AAP's Khajuria.