President Kurmanbek Bakiyev nominated Isabekov after MPs twice rejected the candidacy of former premier Felix Kulov, who resigned late last year after large-scale protests in the Central Asian nation that forced through a series of amendments to the constitution.
Fifty-seven of 61 members in the legislature backed Isabekov's nomination, and four voted against.
Speaking on the priorities of the new Cabinet, Isabekov said: "The activities of the government should be far from politics and focus on economic and financial development," adding that the government would closely cooperate with parliament on all issues.
Isabekov, 46, an economist by training, held various posts in regional authorities in the early 1990s.
He became deputy head of President Bakiyev's administration following the "tulip revolution" that toppled the longtime leader Askar Akaeyv in 2005, and was appointed agriculture minister in June 2006.
The former premier said Friday he approved of the candidacy of Isabekov, who like Kulov represents the country's northern territories, which have traditionally fought for power with the south.