He also called on Bhutanese Foreign Minister of Bhutan Damcho Dorji.
Jaishankar arrived in Thimpu on a three-day official visit on Monday.
It is Jaishankar's first visit to Bhutan in three years and comes after a 72-day-long stand-off between Indian Army and Chinese People's Liberation Army in the Doklam region that ended after both sides agreed on disengagement of troops.
Jaishankar had earlier visited Bhutan in 2015 which was followed by a visit to Bangladesh, Pakistan and Afghanistan on SAARC mission. (ANI)