During the Loktantra Andolan uprising of 2006 Janamorcha Nepal joined the Seven Party Alliance. After the defeat of the regime of King Gyanendra, Janamorcha Nepal was divided. As of December 2006 there were three separate organizations calling themselves Janamorcha Nepal. One group was led by Amik Sherchan, one was led by Chitra Bahadur KC and a third was led by Chitra Bahadur Ale. Each of the three factions had parliamentary representation. Chitra Bahadur KC's group counted with himself, Dilaram Acharya and Hari Acharya. Pari Thapa and Navraj Subedi sided with Chitra Bahadur Ale. Amik Sherchan's sole follower amongst the original RJM/SJM MPs was Lila Mani Pohkrel, but the group got three more nominated members as the interim legislature was formed (Asarphi Sada, Anjana Bisankhe and Kaman Singh Lama). The Sherchan-led JMN retained the membership in the ruling Eight Party Alliance, and when the interim government was formed Giriraj Mani Pokharel and Shashi Shrestha of the JMN(Sherchan) were appointed as Minister and Minister of State of Health respectively.
The Amik Sherchan-group was able to register themselves with the Election Commission as 'Janamorcha Nepal'. The Chitra Bahadur KC-group changed name to Rashtriya Jana Morcha whereas the Chitra Bahadur Ale-group joined the Communist Party of Nepal (Unified).
In August 2008, Sherchan was deposed as chairman of Janamorcha Nepal and suspended for three months, after having urged support for Ram Baran Yadav in the presidential vote. Lila Mani Pokhrel was appointed acting chairman by the Central Committee of Janamorcha Nepal.