Binali Yildirim, 60, who was the sole candidate to run for the party’s third chairmanship of its history, garnered 1,405 out of 1,411 votes in the election held at the at the Arena Sports Hall Sunday in Ankara.
Out of 1,411 votes, six were declared invalid.
Speaking after the congress, Yildirim said: "I promise that I will never drop this sacred flag you have given me as new chairman of AK Party".
Yildirim said the Sunday's congress showed "fraternity" and "unity" for the party, which he called a "family".
"An example of real loyalty has been experienced once more at this congress," Yildirim said.
In addition, Turkish President Recep Tayyip Erdogan congratulated the new chairman in a telegraph.
The new AK Party chairman is now set to replace Ahmet Davutoglu as the country’s next prime minister.
On May 5, outgoing Prime Minister Ahmet Davutoglu announced that he would not stand again for the AK Party chairmanship.
In August 2014, Davutoglu, who had served as foreign minister since 2009, was elected chairman of the party after then-Prime Minister Recep Tayyip Erdogan became president.
Davutoglu became the second chairman of AK Party after 13 years with Erdogan as the leader.
Yildirim, a co-founder of the party in August 2001, has served as transport minister (with other portfolios, including maritime) in five Turkish governments under prime ministers Abdullah Gul, Erdogan and Davutoglu.
Justice Minister Bekir Bozdag read out a message issued before the vote by Erdogan who said his ties to the AK party had been cut when he became president in August 2015.
"But heart bonds with you have never been cut, God willing, will never be cut," Erdogan said in his message.
Erdogan described the congress as "one of the most important democratic maturities of our recent political history".
He said the new chairman and party administration had key duties: overcoming regional and global crises and preparing for a new constitution as well as achieving Turkey's centennial goals by 2023.