He was chosen as Prime Minister for the second time when he succeeded Girija Prasad Koirala, who surrendered in July 2001. A rebellion by King Gyanendra uprooted Deuba in October 2002.
After two different governments, much political challenge for his reclamation particularly in capital Kathmandu, Gyanendra restored Deuba to the position of Prime Minister in 2004.
He was evacuated on February 1, 2005 by King Gyanendra, who broke up the legislature for a long time and seized direct power.
He was sentenced to two years in jail in July 2005 under debasement allegations, yet was along these lines discharged on February 13, 2006, after the counter defilement body that sentenced him was banned. An authority from Deuba's Nepali Congress Democratic Party, Dip Kumar Upadhaya, told the Associated Press that the previous head's discharge was "a triumph for popular government and a mortifying annihilation for the imperial administration"