The aim of this study was to examine the effects of Content and Language Integrated Learning (CLIL) designed according to the First Principles of Instruction (FPI). A 15-h Japanese CLIL course was implemented. A total of 16 university students attended the course and data were collected from multiple sources, including learning tests, questionnaire feedback, and dialogues in group discussions, were collected and examined. Analysis showed that students' learning outcomes, including basic Japanese proficiency, intercultural communication content, and writing skills, were statistically significantly improved. Students had a high level of awareness of the elements of FPI designed in the course. In addition, all the FPI elements had a positive impact on basic Japanese proficiency except for the application element: the problem-centered, application, and integration elements positively impacted intercultural communication content and writing skills. The results show that students displayed individual differences in using the worksheet to summarize their writing ideas. Students spent most of the time in the group discussions in their native language. Even when Japanese was used, individual Japanese words were used rather than whole sentences in most cases. The results of the quantitative and qualitative analyses showed that the use of problem-centered theory FPI had a positive impact on the design of the CLIL. However, attention is needed to students' individual differences and the guidance of students in applying basic language knowledge in problem-centered learning activities. Finally, it notes points that should be considered when designing CLIL in the future.