Pratheepa completed her undergraduate degree in Statistics and Operations Research at the University of Peradeniya in Sri Lanka. She then was a lecturer in statistics at the University of Peradeniya before pursuing graduate studies. She received an MS in Statistics and a Ph.D. in Mathematics with an emphasis in Statistics from Texas Tech University. While completing her Ph.D., she interned at the Research and Testing Laboratory in Lubbock and the Clinical Research Institute at Texas Tech University Health Sciences Center. Pratheepa completed postdoctoral training in the Department of Statistics at Stanford University focused on developing statistical and computational methods for analyzing high-throughput sequencing data. She taught undergraduate courses at Texas Tech University and Stanford University.