This study aims to find out the challenges of effective teaching of chemistry. It tries to explore the areas of challenges that chemistry teachers face for delivering the chemistry content effectively and to find out the student’s difficulties in catching the chemical understanding. The study performed among the purposively selected ten secondary level chemistry teachers of Kathmandu valley, Nepal. Information generated with the help of interview questionnaire and the responses of the teacher were recorded. The responses were classified based on various factors, the matrix of which was prepared for the analysis. The challenges for effective teaching of chemistry was found in several areas like teaching methods, classroom size, interest of students, classroom environment, development of chemical concept, gap in the curriculum, evaluation system, professionalism of chemistry teachers, and laboratory work. Study established that teacher related factors and school environment plays important role in the effective teaching of chemistry. Government and other stakeholders in education should improve the teaching-learning environment of students and motivate teachers. Curriculum planner and chemistry experts should consider the areas, which help in effective implementation of chemistry curriculum, which will help students to active better at chemistry.