Halwathura was born 4 February 1978 in Kalutara, Sri Lanka. He was raised in a family of four consisting of his parents and his younger brother, Shanaka Halwathura, a Sri Lanka Army officer. He attended Kalutara Vidyalaya National School. Halwathura graduated with first-class honors from the University of Moratuwa with a bachelor’s of science in engineering. He later completed his doctorate degree in structural and building services engineering in 2008 from the same institution.