Project-based learning (PjBL) has been increasingly promoted and extended to online environments to enhance the quality of higher education. However, PjBL involves complex processes requiring higher-order thinking skills, which may pose challenges to many students especially in online settings with little prompt support from teachers. The problem may compromise the learning of low-achieving students, who often have inadequate higher-order thinking skills. Visible thinking approaches have the potential to make higher-order thinking processes accessible to students. This study was conducted with 72 university students who engaged in visible thinking supported online PjBL of computer programming. A one-group pretest-posttest design was adopted to compare the learning outcomes among high-, medium- and low-achieving students. The results showed that compared to high and medium achievers, low-achieving students made the most progress in product quality and thinking skills (in particular process design skills). They performed almost as well as medium and high achievers in product quality and process design skills at the end of the study. They also gained more knowledge from the project than high achievers did. Moreover, compared to medium achievers, low achievers perceived the approach as more valuable, made more effort on the study, and felt more competent in completing the project. The findings reveal the promising effects of visualizing higher-order thinking processes in narrowing the achievement gap between high and low achievers, offering all students an equal chance to engage in effective learning with projects.