This paper presents a brief introduction of the science education in Japan with an overview of the educational contents and standards laid by the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT). It highlights the results of the International Education Association (IEA) on science education in Japan at upper secondary school level which revealed that science was still not being learnt directly from natural things and phenomena. In order to investigate the strategic methods on the smooth transition of science education from the upper secondary school to the university, an overview of school education in Japan is presented including the accompanying issues and concerns. The examples and criteria for good practices together with the syllabus on the related subjects are discussed. The keys to improve teaching and learning on the contents and methods were integration, scientific literacy, close relations with daily life, communities and families, audiovisual or information and communication technologies (ICTs) and relevant pedagogy to motivate and expand students' own views coping with the changing society. Finally, four recommendations are described to address the general concerns so as to improve university science education in Japan.