She was born to K. P. Balamurali and Sobha Balamurali. Her father Balamurali is a music director who has composed several musical albums, while her mother Sobha is a lawyer who has also worked as playback singer in some Malayalam films. Singer-composer K. P. Udayabhanu is her paternal great-uncle.

Aparna is trained in Indian classical music and classical dance styles such as Bharatanatyam, Mohiniyattam, and Kuchipudi. She studied architecture at Global Institute of Architecture in Palakkad.