Nikhil Banerjee was born on 14 October 1931 in Calcutta. His father, Jitendranath Banerjee, was an amateur sitarist and Banerjee was fascinated by his father's playing. Although he wanted to try his hand at an instrument as early as the age of four, he was discouraged by his father and grandfather. At the age of five, however, they relented and he acquired a small sitar, initially learning under his father. Banerjee grew into a child prodigy. He won an all-India sitar competition and became the youngest musician employed by All India Radio at the age of nine. Jitendranath approached Mushtaq Ali Khan to take Nikhil as a disciple, but only learned from this master for a few short weeks. Instead Birendra Kishore Roy Chowdhury, the zamindar of Gouripur in present-day Bangladesh, became responsible for much of his early training. He also had considerable training under Pt. Radhika Mohan Maitra, before he went under the discipleship of Ustd. Allauddin Khan.