The purpose of this paper is to gain deeper insights into the way Social Studies programs are structured and taught in two national universities; one from Botswana and the other one from Nigeria; including, the extent of the infusion and presentation of contemporary issues in their Social Studies programs, program similarities, and the challenges faced by lecturers in the teaching of topics related to contemporary issues at the undergraduate level. Using a case study approach, this paper examines how contemporary issues, such as HIV/AIDS, drug abuse, child abuse, social policy, violence, reproductive health, climate change, to mention a few, are infused in the Social Studies programs of the two institutions under study, one each from Nigeria and Botswana. Methods of data collection were both qualitative and quantitative and they included case study of the Social Studies programs at the two universities. It was found that the Social Studies programs were structured along the use of integrated methodology with the infusion of contemporary issues across their courses with a high degree of similar content areas and challenges. The recommendations focused on the availability of teaching materials, enlarged classroom space, regular workshops, the use of external examiners, regular program reviews, among others.