In 1991, Balakrishna acted in a science fiction film Aditya 369, directed by Singeetam Srinivasa Rao. A sequel, tentatively titled Aditya 999, has been planned but not yet confirmed. This was the only science fiction film in Telugu cinema during that period of time. He then had two releases in 1992, Dharma Kshetram and Rowdy Inspector, directed by B. Gopal. In the year 1993, he had two releases on the same day, which are Nippu Ravva, alongside Shobana, Vijayashanti, directed by A. Kodandarami Reddy, Bangaru Bullodu, alongside Raveena Tandon and Ramya Krishna, directed by Ravi Raja Pinisetty. His next appearance was a folk role in Bhairava Dweepam in 1994, directed by Singeetam Srinivasa Rao. The film was a critical and commercial success and one of the milestones of his acting career. In Brahmarshi Viswamitra, directed by his father, he played as Satya Harischandra and Dushyanta. Between 1994 and 1999, he acted in movies such as Bobbili Simham, Vamshanikokkadu, Peddannayya and moderate successes such as Muddula Mogudu, Maato Pettukoku, Raana and Pavitra Prema. In the year 1999, he acted in B. Gopal's action film Samarasimha Reddy, opposite Simran and Anjala Zhaveri.