The flipped classroom had shown positive effects on academic achievement and student satisfaction, but require a higher level of self-regulation from students. There are few studies about flipped classroom characteristics that could help to improve self-regulation. This study assess the influence of choice in the goal setting process of students and their perception of clear goals while learning in flipped classes, in comparison with lecture based courses in a university-level programming class (n = 299). A method based in the progression mechanism of role playing games is used to help the goal setting process of students in the flipped classroom. Students in flipped classes perceived higher levels of choice in comparison with students in lecture based courses. The effect of choice on achievement was partially mediated by the perception of clear goals of the students and was higher in lower performing students. Our results suggest that the increased perception of choice in the flipped classroom, and their effect in achievement, complement the effect of active learning in the results obtained from flipped classroom use. Instructional designers can use the flipped classroom to provide choices to help the goal setting process of students.