On 30 October 2006, Pokharel began working as the Chief Election Commissioner (CEC) of Nepal. At 11 o'clock he entered the Bahadur Bhavan—the home of the Election Commission, which had been built in the nineteenth century by a Rana Prime Minister. He was met by the Secretary of the Election Commission, Dolakh Bahadur Gurung, who escorted him to his office.

Gurung advised him that the first task was to get the government to finalise legal framework, including the constitution and electoral laws. But there was also the question of rebuilding the trust of the political parties and other partners, which the last election—commissioned by King Gyanendra—had destroyed. This would be difficult, given the prevailing post-conflict political environment.

Soon after the Chief took office, other commissioners were appointed—Usha Nepal, Neil Kantha Uprety, Dolakh Bahadur Gurung and Ayodhi Prasad Yadav. These appointments were unofficially shared between the main four political parties representatives of the Democratic bloc and the Maoist party.

As soon as the commissioners had been appointed, the Chief held a meeting. He briefed them, saying: