In the current history, diplomacy as the practice of conducting foreign relations between states through official representatives and peaceful methods had different types. Today, as a result of technological revolution, the importance of science and technology has been raised and most of politicians tend to use it as an instrument in developing their nation’s foreign policy. Hence, it seems that a new kind of diplomacy approaches and it can be labeled Science and Technology Diplomacy. In the age of Globalization and Interdependence, it will be one of the best devices to formulate and execute foreign policy as well as following national interests beyond the boundaries. During the last decades science and technology have been improved outstandingly in Islamic Republic of Iran. Due to the great stance of the neighbors in the Iranian foreign policy and common economic, cultural and historic relations in the past, we can conduct this kind of diplomacy in Afghanistan. Our focus, in this paper, is on the main challenges and opportunities that may be exist on conducting Science and Technology Diplomacy of Iran in Afghanistan. We concluded that despite of many ongoing challenges, there are so many factors that will facilitate the scientific and technologic presence of Iran in Afghanistan. Undoubtedly, removing the obstacles in conducting this kind of diplomacy in Afghanistan, will promote the political and economic relations between these two Islamic countries.