Pachauri submitted his resignation to Prime Minister Manmohan Singh after his Rajya Sabha term ended on April two, sources said.
There has been speculation about Pachauri making an exit from the Cabinet.
Pachauri, elected from Madhya Pradesh for several terms, could not return to the Upper House as the party had no strength in the assembly there to ensure victory of even a single candidate.
Pachauri was recently appointed to the crucial post of PCC chief in Madhya Pradesh in view of the state going to elections later this year.