Raghavan, who served as Deputy High Commissioner in Islamabad about a decade ago, crossed via the Wagah land border.
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.
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A report in the Pakistani media said Raghavan would have to wait for some time for presenting his credentials since President Asif Ali Zardari is away from the country on a private visit.
The wait could be longer if Zardari opts to stay abroad till the expiry of his term in about six weeks, The News daily quoted its sources as saying.
If Zardari does not return to Pakistan till September, Raghavan will have to wait for the election of a new President to submit his credentials.