Bishnu Bahadur Manandhar (general secretary of CPN(United)) was named general secretary of the party (he later stepped down) and Prabhu Narayan Chaudhari (president of CPN(M)) is the president of the party. Other politburo members were:
Hemant Bahadur B.C.
Lok Narayan Subedi
Chandra Deo Joshi
Sharan Bikram Malla
Bhim Prasad Sedhai
The founding unification conference also elected a 34-member Central Committee and a 82-member National Council.
In mid-October 2006, the party went through an internal crisis. Prabhu Narayan Chaudhuri received harsh criticism from party members over his actions as Minister of Land Reforms. On October 14 he was gheraoed in his office by party cadres. Ten politburo members, including both Manandhar and Chaudhuri, resigned. Chandra Deo Joshi was appointed acting chairman whereas Lok Narayan Subedi became the new general secretary of the party.