A 1981-batch Indian Foreign Service officer, Gokhale succeeds S Jaishankar.
Gokhale served as secretary (economic relations) in the Ministry of External Affairs (MEA) before taking up the new role.
As foreign secretary, he will face multiple challenges including improving ties with countries such as Nepal, Maldives, Sri Lanka and Myanmar in India's neighbourhood, where China has been seeking to expand its influence.
It will also have to be seen whether he brings certain changes to India's approach in dealing with Pakistan.
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He was India's Ambassador to China from January 20, 2016, to October 21, 2017, before moving back to the MEA headquarters here.
His earlier diplomatic assignments include postings in Hong Kong, Hanoi, Beijing and New York. He had also served as Deputy Secretary (Finance), Director (China and East Asia) and Joint Secretary (East Asia) during his stints at the MEA here.
He was High Commissioner of India to Malaysia from January, 2010, to October, 2013, Ambassador of India to the Federal Republic of Germany from October, 2013, to January, 2016, and Ambassador of India to the Peoples Republic of China from January, 2016, to October, 2017.
Earlier this month, the Appointments Committee of the Cabinet headed by Prime Minister Narendra Modi approved the appointment of Gokhale to the post of foreign secretary.
Jaishankar was appointed foreign secretary in January, 2015, for two years, just a few days before his retirement. He replaced Sujata Singh, whose term was abruptly cut short by the government.
A 1977-batch IFS officer, Jaishankar was given a one-year extension in January last year.
US envoy Ken Juster congratulated Gokhale as he took charge of the top post.
He also congratulated Jaishankar on his three year-long tenure.
"Congratulations Foreign Secretary Dr. S Jaishankar on your great tenure! You are an exemplary diplomat and long-time friend. It has been an honor and pleasure working with you in strengthening #USIndia relations. Good luck my friend!," Juster said.