Ekanayaka holds a Bachelor of Arts (Honours) degree from the University of Peradeniya and a Master of Science degree and PhD from the University of Edinburgh. She is a Fellow (FTCL) of the Trinity College of Music (UK), a Licentiate (LRSM) of the Royal Schools of Music (UK) and Licentiate (LGSMD) of the Guildhall School of Music & Drama (UK) which awarded her its Professional Performer's Diploma (PPD) in 1999.
