The accusation comes days after he was awarded a newly-created senior post at his think tank The Energy and Resources Institute in Delhi (TERI).
He was removed as its head last July when another employee accused him of harassment - an allegation he denies.
The latest complainant said she spoke out after news of his new job emerged.
In a statement issued by her lawyers, the former employee said the harassment included "sexually loaded remarks", kissing her forcibly and "intrusive questions" about her personal life.
She described him as a "serial sexual harasser" and said harassment by Mr Pachauri was an "open secret" in the think tank.
The woman, who joined TERI in 2003 and worked there for over a year, said she was forced to speak out after Mr Pachauri's "big promotion", reports said.
Mr Pachauri's lawyer Ashish Dixit told the Press Trust of India news agency that he had not seen the second complaint and could not comment.
Earlier this week TERI appointed Mr Pachauri to a newly-created post of executive vice chairman, after his successor took over his previous position as director general.
After the first accusation was made, a court barred Mr Pachauri from TERI's offices. It later allowed him to return while still on bail, on condition that he stay away from his alleged victim. He was also removed as chief of TERI for a year.
But the move  to create a new role for him sparked widespread outrage.
He resigned as the head of the UN climate change panel in February last year in the wake of the allegations.
In 2007 he collected the Nobel Peace Prize on behalf of the organisation, for its work in the scientific assessment of the risks and causes of climate change. The IPCC shared the award with former US vice-president and environmental campaigner, Al Gore.
A second woman has stepped forward to accuse the former head of the UN climate change panel, RK Pachauri, of sexual harassment.