Agricultural supply chain management includes all the events involved in moving products of the agricultural sector from the field to the customer, and is a crucial aspect ensuring the rich contribution of the agricultural sector to the economic growth of the nation. The purpose of this paper is to add value to the present knowledge base by ascertaining the challenges of the agricultural supply chain in India on the basis of a thorough literature survey and the Delphi technique. Following this, the decision-making trial and evaluation laboratory approach was used to model the identified challenges, explore the cause–effect interrelationship, and to develop the systematic hierarchical structures of challenges through an interpretive structural modeling methodology. The implementation of the approach in the Indian context led to the inference that two factors, namely limited integration among the national agricultural markets, and limited agricultural market infrastructure were the most important ones. The integrated model obtained as an output of this study intends to guide the agricultural policy- and decision-makers to improve the performance of the agricultural supply chain in India. Also, some essential recommendations have been given to improve the efficiency of the agricultural supply chain management.