Announcing his appointment, US Secretary of State John Kerry said, "He has deep and longstanding relationships in the region and I couldn't be more grateful that Jim has agreed to take on this assignment."
He said that he called the leaders of the two countries to inform them of his decision in this regard.
Kerry called Afghan President Hamid Karzai, Pakistan President Asif Ali Zardari and Pakistan Army Chief, Gen Ashfaq Pervez Kayani, according to a State Department spokesman.
Dobbins was the first US diplomatic envoy to Afghanistan after the fall of the Taliban.
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He represented the United States at the Bonn Conference that established the new Afghan Government, and he raised the flag over the US Embassy in Kabul when it reopened in 2001, Kerry said.
Currently the director the RAND International Security and Defense Policy, Dobbins succeeds Marc Grossman, who resigned from the post last December.
Among his many assignments, he served as assistant secretary for European affairs, as well as special assistant to the president and special adviser to the president and secretary of state on the Balkans, and as ambassador to the European community.