Raghavan was given a send-off at the border with India's Deputy High Commissioner J P Singh and other senior Embassy officials in attendance.
Raghavan on Tuesday had paid a farewell visit to Prime Minister Nawaz Sharif, who had appreciated his services for improving ties between the two countries.
He was appointed High Commissioner to Pakistan in June 2013 when new government led by Sharif was formed after historic peaceful transition of power from one civilian government to another.
He is being replaced by Gautam Bombawale who is currently serving as ambassador to Bhutan.
Bombawale is expected to take on his duties as India's High Commissioner to Pakistan by mid-January, sources said.