Sri Vishvaksena Temple is located at the northern side of the main temple, in the Mukkoti Pradakshinam.
Sri Vishwaksena occupies an important place in the Vaikhanasa Agama.
In Vaishnavite functions and temple rituals, Sri Vishwaksena is worshipped first.
Vishwaksena is said to be the chief of the army (of the Lord) and is believed to protect the function or ritual from evil.
The idol of Vishwaksena and its worship are strictly in accordance with the Vaikhanasa Agama. During the daily worship of Lord Venkateswara, the garlands and flowers (called nirmalya) from the Lord's idol are removed and Vishwaksena is worshipped with them.
Before commencement of the annual Brahmotsavam, the Senadhipathi or Vishvaksena Utsava is performed followed by Ankurarpana. His idol is also taken out in a procession during the Adhyayanotsavam.