In the Philippines, inquiry-based teaching has been promoted and implemented together with recently instigated curriculum reforms. Serious teacher professional development efforts are being used extensively to properly orient and present the benefits of inquirybased teaching. Despite these efforts, there still exists a big gap in the effective implementation of inquiry-based teaching in the classroom. Lesson study, a professional development model which started in Japan, has increased in popularity among education specialists as they recognise its capabilities in building a sustainable, collaborative, and reflective professional development for in-service teachers. In this study, the lesson study framework was used to identify three challenges in implementing inquiry-based teaching in elementary school science education in the Philippines, namely, a lack of support, training, and availability of inquiry-based materials; an overemphasis on assessing content learning rather than learning through inquiry; and the difficulty and time consuming nature of inquiry approaches.