This study examined the relationship between pre-service teachers’ science learning competence and learner autonomy and whether these constructs differed by teacher education program and grade level. Using a correlational survey design, data were collected from 341 pre-service teachers enrolled in preschool, primary, and science education programs. The Competence Scale for Learning Science and the Learner Autonomy Scale were used for data collection. Data were analyzed using one-way ANOVA and Pearson correlation analysis. Science learning competence differed significantly by teacher education program and grade level, with preschool education pre-service teachers reporting higher scores than primary and science education pre-service teachers. Learner autonomy also differed across programs and grade levels. Preschool education pre-service teachers reported higher overall learner autonomy than science education pre-service teachers, while third- and fourth-year pre-service teachers scored higher than second-year pre-service teachers. Science learning competence was weakly and negatively related to learner autonomy. The findings suggest that science learning competence and learner autonomy are related but distinct aspects of pre-service teachers’ learning.