British Council for East Asia reported that the level of English competency of Indonesian pupils in primary and secondary education in English lessons and other scientific disciplines was very concerning. They did not use English as Medium Instruction (EMI) in Science class well. Besides, pupils need to have English communication skills in the 21st century. Because of that, the research aims to investigate how EMI should be applied in Science class. The purposive survey method was used in this study involving the process of data triangulation from tests, questionnaires, unstructured interviews, and observations of learning. The research subjects were selected by a purposive sampling technique involving 172 pupils aged 11-13 years from several secondary schools in four major cities in Indonesia which use English as the medium of instruction in Science class. The results showed that EMI can be applied in Science class by bilingual strategies. Most of the pupils understood the teachers' instruction, scientific terms, even scientific concepts but they felt safer using both Indonesian and monolingual languages to avoid some errors e.g. misconceptions when teachers explain fundamental science concepts. Introducing keywords in the form of bilingual terms related to the fundamental concepts of science helps pupils to understand science concepts more deeply and develop pupils' ability to speak English actively. These findings are expected to become a reference for how to use EMI in science class.