This paper examined the effect of religion on educational system in Nigeria and its implication on sustainable educational goal. It is pertinent to ascertain the extent at which religions has affected virtually all institutions especially in Nigeria. In this study, ethno religious crisis which in most cases resulted into disturbances, attacks, violence is emphasized. Thus, consequences of religious crisis, needs educational goals, ethnicity and religion were critically discussed in this context. Therefore, good governance should be accorded high priority to forestall proper security in Nigeria. While traditional and religious leaders should help curtail crisis in their domain so as to promoting Harmony and peaceful coexistence in our society.