The adoption of blended learning at university levels is pervasive. This learning approach is deemed to be more effective compared to face-to-face or online learning. To prove the claim, this study aimed to investigate a gap that may be existed between students’ expectations and perceptions of blended learning implementation at the Science Department in a university in Surabaya, Indonesia. A questionnaire and semi-structured interviews were utilized to gather relevant information from 79 preservice science teachers who have experienced blended learning in science subjects. The gaps between expectations and perceptions were measured using Cohen’s effect size. Overall, the effect size of students’ expectations and perceptions of the blended learning implementation exceeded 0.5 and is categorized as large. The aspects with large effect size values included the number of interactions between students and teachers. These findings indicated that the implementations of blended learning in science subjects were not run well.Implications of this study are discussed.