Effect of student’s motivation towards learning science has been studied through various research works. This study centered to investigate the motivation of students in secondary rural schools in Sri Lanka towards learning different branches of science. Secondary school students in grade 11 were involved and the main area namely Biology, Chemistry and Physics in science subject thought for GCE ordinary level examination were considered as the main branches of the science for the study. The current study is an empirical study in which 160 of randomly selected rural secondary school students were involved. A self-prepared questionary was used as the research instrument for this quantitative survey. Stratified sampling method was used as the sampling method and the sample includes rural secondary school students in Palugaswewa education division located in Anuradhapura district, Sri Lanka. A significance level of motivation was shown for the biology in which female students became prominent.