Abstract: Recently, the use of learner centered pedagogy was adopted to improve the teaching and learning process. However, its successful implementation is challenged by different factors. In this regards, this research was aimed at investigating the challenges encountered in using learner centered pedagogy for teaching mathematics secondary schools of Rulindo District in Rwanda and the possible strategies adopted by mathematics teachers. Both qualitative and quantitative data were collected both randomly and purposefully from a sample of 240 students and 16 mathematics teachers selected from 4 secondary schools. The above data was collected by using Likert scale questionnaire, interview guide and classroom observation. For ensuring the validity and reliability of data collection tools, they were piloted in secondary schools of Gicumbi District after which the Pearson correlation coefficient (r) and Cronbach Alpha (α) were computed. All questions were adjusted to have r>0.5 and data collection tool was reliable as α was 0.87 that is greater than 0.7. The obtained data were analysed both descriptively and thematically. Different challenges were realized in using learner centered pedagogy for teaching mathematics. These include, overloaded classrooms, overloaded syllabuses, poor student background, insufficient training and inadequate ICT tools. Different strategies including the use of groups of students with differentiated capacities, empowering CPD culture and peer learning within close schools were adopted. The use of effective strategies for effective implementation of learner centered pedagogy were recommended.