This study focuses on analyzing the content and structure of the “Atomic Physics” course in higher education institutions of the Republic of Kazakhstan. Based on university curricula and official documents, a content, statistical, factor, and comparative analysis was conducted. The results revealed significant differences in the way the course is taught across universities, particularly in terms of credit allocation, semester workload, the ratio of lectures, practical and laboratory sessions, as well as in the qualifications of teaching staff and academic opportunities. A survey involving 93 students demonstrated that the structural efficiency of the course, material and technical resources, teachers’ methodological competence, and financial accessibility were evaluated positively (mean values ranged between 4.2–4.4, Cronbach’s alpha coefficient between 0.906–0.944). These findings indicate that, while students generally support the program, there is a clear need for further improvement. In the experimental section, the STEM approach was considered as an effective tool for linking the course content with practice. It was found that the integration of STEM enhances students’ deeper understanding of the discipline, develops their research and project skills, fosters engineering thinking, and strengthens digital technology competencies. In conclusion, the modernization of the “Atomic Physics” course through STEM integration contributes to improving the professional competence of future physics teachers, enhancing the quality of national education, and aligning the educational system with international standards.