An issue that continued to threaten the election, and which was a constant headache for the Commission—was the electoral system.

The main Constituent Assembly Member Election Act, passed in June 2007, had established a mixed electoral system with a Constituent Assembly of 497 members—240 of whom would be elected through the First-Past-The-Post (FPTP) system and 240 through the Proportional Representation system. Additionally, seventeen members would be appointed by the Council of Ministers. Voters would get two ballots, voting separately in the FPTP and the PR races, and each element of the election would be counted separately. Decision on this process was reached by the parties after a series of negotiations.

It had to be agreed that the nature of the electoral system was critical, not least because it had been the focus of the Maoists' armed struggle. Since the restoration of multiparty parliamentary democracy, in early 1990, Nepal had adopted a majoritarian system, known as the First-Past-The-Post for its three parliamentary elections in 1991, 1994 and 1999 as well as for its two local elections in 1992 and 1997. In this system—practiced, for example, in the UK and India—candidates with the highest number of votes in a constituency are elected. Unfortunately, this system failed to meet the aspirations of Nepal's diverse society, which consisted of over 100 ethnic groups, speaking multiple languages.