He is reported to have submitted his resignation to the High Court.
Reacting to the development, Hyderabad MP and AIMIM chief Asaduddin Owaisi said he was surprised with NIA judge Ravinder Reddy's decision.
"Judge who gave acquittal to all accused in Mecca Masjid Blast RESIGNS very intriguing and I am surprised with the Lordship decision," Owaisi wrote on Twitter.
The National Investigation Agency court held that none of the charges framed against the accused, including Swamy Aseemanand, had been proved, a lawyer for one of the accused told reporters outside the Nampally criminal court complex.
Righwing Hindu activists Nabakumar Sarkar alias Swamy Aseemanand, Devender Gupta, Lokesh Sharma, Bharat Mohanlal Rateshwar alias Bharat Bhai and Rajender Chowdhary, against whom the charges were framed, were all acquitted.
Swamy Aseemanand, a resident of Gujarat and head of Vanvasi Kalyan Ashram, was earlier acquitted in the Ajmer Dargah blast case and is currently on bail in Samjhauta Express blast case of 2014.
Devendra Gupta is the RSS parcharak from Bihar while Lokesh Sharma is a RSS activist from Madhya Pradesh.
The powerful explosion had killed nine people and injured more than 50 during the Friday prayers at the 17th century mosque near the iconic Charminar on May 18, 2007.
Two live IEDs were also recovered by police and defused. Later, five more people were killed in subsequent police firing on the crowd outside the mosque.
There were a total of 10 accused in the case and five of them were chargesheeted by the NIA. One, Sunil Joshi, a RSS pracharak, was murdered during the course of investigation. Three accused, Sandeep V Dange and Ramchandra Kalsangra, both RSS activists, and Amit Chowhan, are absconding while Tejram Parmar is on bail.
A total of three chargesheets were filed by the Central Bureau of Investigation (CBI) and the NIA in the sensational case. Over 200 witnesses were examined and 400 documents were submitted to the court.