A bomb planted on a motorcycle went off at Malegaon in Maharashtra's Nashik district on September 29, 2008, killing six persons and injuring 101 others.
The investigation was initially conducted by the state Anti-Terrorism Squad, which had pinned the blame on right-wing extremists who were members of 'Abhinav Bharat' group.
The probe was later handed over to the National Investigation Agency, which gave a clean chit to Thakur. However, the court conducted the trial against her, citing prima facie evidence.
A special court in Mumbai on Thursday acquitted all seven accused, including former BJP MP Pragya Singh Thakur and Lieutenant Colonel Prasad Purohit, noting there was "no reliable and cogent evidence" against them.