Given the evolution in the agricultural sector and the new challenges it faces, managing agricultural supply chains efficiently has become an attractive topic for researchers and practitioners. Against this background, the integration of uncertain aspects has continuously gained importance for managerial decision making since it can lead to an increase in efficiency, responsiveness, business integration, and ultimately in market competitiveness. In order to capture appropriately the uncertain conjuncture of most agricultural real-life applications, an increasing amount of research effort is especially dedicated to treating uncertainty. In particular, quantitative modeling approaches have found extensive use in agricultural supply chain management. This paper provides an overview of the latest advances and developments in the application of operations research methodologies to handling uncertainty occurring in the agricultural supply chain management problems. It seeks to: (i) offer a representative overview of the predominant research topics, (ii) highlight the most pertinent and widely used frameworks, and (iii) discuss the emergence of new operations research advances in the agricultural sector. The broad spectrum of reviewed contributions is classified and presented with respect to three most relevant discerned features: uncertainty modeling types, programming approaches, and functional application areas. Ultimately, main review findings are pointed out and future research directions which emerge are suggested.