E-learning media is one effective solution as a learning tool that could be implemented anytime and anywhere. Science, Technology, Engineering, and Mathematics (STEM) approach through the use of elearning is expected to develop students Higher Order Thinking Skills (HOTS). This study aimed to measure students HOTS abilities through the use of e-learning based-STEM media in quantum physics courses. Through purposive sampling technique set sample research that is students who are in the program of quantum physics courses for ten people in the even semester 2017-2018 in Jurusan Pendidikan Fisika Universitas Papua. The instruments used are eight numbers of HOTS questions in theform of essays and questionnaires of student responses given after the lesson. The data analysis technique used was gain test to see if there was the improvement of HOTS student ability and hypothesis test through SPSS to know the difference of HOTS ability before and after learning, while student response questionnaire analysis is done through Rash modeling using the Winstep program. The results showed that the value of N-gain (0.7) high category and Wilcoxon test significance value (0.004) indicating that learning of quantum physics through e-learning based on the STEM can improve students HOTS capability. Rasch modeling showed that in general the students strongly agree on the learning done. Therefore, the implementation of e-learning based on the STEM in quantum physics course could be used as one of the references to develop students HOTS capability.