A 1981-batch Indian Foreign Service officer, Gokhale is currently serving as the secretary (economic relations) in the Ministry of External Affairs (MEA).
Gokhale will take charge tomorrow, a senior MEA official said.
Gokhale, considered an expert on China, had played a key role in negotiations to resolve the 73-day-long Doklam standoff between Indian and Chinese armies last year.
He was India's Ambassador to China from January 20, 2016 to October 21, 2017, before moving back to the MEA headquarters here.
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He has held the posts of director (China and East Asia) and then joint secretary (East Asia) in the MEA.
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, replacing Sujata Singh, whose term was abruptly curtailed by the government.