The youngest of five children, Ngqawana started playing flute at the age of 21. He dropped out of school prior to meeting university entrance requirements but won entrance to a place at Rhodes University. He later studied for a diploma in Jazz Studies at the University of Natal. He was offered scholarships to the Max Roach/Wynton Marsalis jazz workshop and later a scholarship to the University of Massachusetts Amherst, where he studied with jazz musicians Archie Shepp and Yusef Lateef.
After his return to South Africa in the 1990s Ngqawana worked with South African jazz musicians Hugh Masekela and Abdullah Ibrahim. He was featured on Bjorn Ole Solburg's Norwegian San Ensemble album, San Song. He toured the United States with his band "Ingoma" in 1995, and he made an appearance at Black History Week in Chicago.
He performed a duet with poet Lefifi Tladi in the documentary Giant Steps (2005), directed by Geoff Mphakati and Aryan Kaganof. In January 2010, Ngqawana's Zimology Institute was vandalised by scrap metal thieves. He performed a duet concert in the rubble of the vandalised building with Cape Town pianist Kyle Shepherd. This performance was filmed as The Exhibition Of Vandalizimiop by Aryan Kaganof. The Vandalizim concerts were subsequently performed at the MOMO Gallery in Johannesburg and at a scrapyard in Stellenbosch, organised by Stellenbosch University's music department and DOMUS.