Speaking to the media after he crossed over to Pakistan via the Wagah land border, Raghavan said India wants good and friendly ties with Pakistan that will benefit the people of both countries.
He said measures should be taken to address the menace of terrorism. Both countries should also build trade and cultural relations, he added.
Terrorism has been a key irritant in India-Pakistan relations since the 2008 Mumbai attacks, which were carried out by the banned Lashkar-e-Tayiba.
Indian officials have called for the speedy prosecution of Pakistani suspects charged with involvement in the attacks, whose trial has progressed at a snail's pace.
Raghavan and his wife were greeted by Pakistani officials at Wagah.
A diplomat with considerable experience of Pakistan affairs, Raghavan served as Deputy High Commissioner in Islamabad about a decade ago.
He will replace Sharat Sabharwal, who was given several extensions after he reached the age of retirement last year.
Sabharwal returned to India earlier this month.
During his last stint in Pakistan, Raghavan served under Shivshankar Menon, who went on to become the Foreign Secretary.
An officer of the 1982 batch of the IFS, Raghavan has wide-ranging experience of Pakistan affairs and is highly regarded by Pakistani intellectuals and politicians.
He is well known in the Pakistani capital, where he has many friends.