Reading education and reading affective factors significantly affect school-age students’ academic achievement. Nevertheless, most teachers disregard scientific strategy-based reading instructions and scholars have recently regarded L2 reading affective factors, namely reading motivation and anxiety. Moreover, technology-aided EFL reading courses for primary schoolers have been neglected. Accordingly, the current study aimed to implement seven L2 reading strategies suggested by Yapp et al. (2021a), and evaluate the effect of these strategies on English reading comprehension, motivation, and anxiety at virtual environment by using online team-teaching. The EFL fifth graders and pre-service teachers of the study were selected via volunteer sampling. The students (n = 28) were randomly assigned to two groups (n = 14 for each group) and the teachers (n = 4) were randomly assigned to two groups (n = 2 for each group) as well. One group was given Traditional Instruction (TI) and taught by two instructors whereas the other group received Strategy-Based Instruction (SBI) and was taught by the other two instructors. To assess L2 reading motivation and anxiety, the questionnaires by Dhanapala (2008) and Saito et al. (1999) were administered. The within- and between-group analyses using paired-sample t-tests and ANCOVAs indicated that although both groups’ reading comprehension, motivation, and anxiety were enhanced, the SBI participants outperformed the TI participants. Moreover, the interview with the SBI group demonstrated their positive attitudes toward the SBI course. The current study would encourage EFL teachers to base reading instruction upon reading strategies when teaching young EFL learners.