The use of E-learning Madrasah is a means of delivering online learning materials to students, which is very flexible to use when studying anywhere and anytime. The aim of this study was to find out the teachers' challenges in using E-learning Madrasah at MAN 1 Pangkalan Balai, Banyuasin. This study was investigated by using qualitative research design with two teachers as the participant taken by using purposeful sampling method. The data were collected by using in-depth interviews, and were analysed by using thematic analysis technique. The result of the study revealed that there were some EFL teachers' challenges in using E-learning Madrasah, such as: (1) EFL teachers' capability in managing the web based (E-learning Madrasah), (2) Web management, (3) Limited Connection, (4) Technical issues, (5) Pedagogical matters, and (6) Teachers' lack of motivation in using web due to the school system. Additionally, this study recommends that the challenges faced by teachers using Madrasah E-learning as a teaching medium can be found that the constraints are more on signals and lack of time but can be minimized by communication and finding other teaching alternatives.