The Indian Union Muslim League strongman won by 171,023 votes. He got 515,330 lakh votes, the highest anyone has secured in the constituency in northern Kerala.
M.B. Faisal of the Communist Party of India-Marxist (CPI-M) got 344,307 votes. The Bharatiya Janata Party (BJP) candidate N. Sreeprakash finished a distant third with 65,675 votes.
As Kunhalikutty came out of his home, jubilant supporters shouted slogans hailing him and lifted him on their shoulders.
Kunhalikutty said his party led even in village councils controlled by the Left.
"This is because the electorate has placed faith in me as I spoke about the need for a secular outlook. Also, the unity (in the Congress-led) UDF helped us."
The IUML leader added: "Literate Kerala has voted for secular politics. Kerala's vote has never been on communal lines."
He said the BJP was the biggest loser in the contest while the IUML bounced back strongly in the assembly segments Perinthalmanna and Mankada where it had performed poorly in the 2014 Lok Sabha polls.
Kunhalikutty remained far ahead of his nearest rival -- the young Faisal -- throughout the counting process.
The April 12 election was necessitated by the death of IUML MP and former central minister E. Ahamed.
Malappuram is an IUML citadel and Ahamed won in 2014 with a record margin of 1.94 lakh votes.
Kunhalikutty secured 55.04 per cent of all votes, compared to Ahamed's 51.28 per cent.
The Left's vote share went up from 28.47 per cent in 2014 to 36.77 per cent. The Bharatiya Janata Party's vote share dipped from 7.59 per cent to 7.01 per cent.
The IUML is the second biggest partner in the Congress-led United Democratic Front (UDF), which was ousted from power in Kerala last year.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)