The large volume and diversity of research sources related to the challenges affecting the efficient operations of FSCs demand a systematic literature review to explore the tools employed to address such challenges and to identify research gaps for future research. Our review of the FSC literature covered 141 articles published over the period 2010-2021. It was found that advanced technologies and optimization models were the most predominant tools for addressing FSC challenges with 40% of the articles embracing IOT-based technological frameworks and 56% of the reviewed papers deploying mathematical and computational optimization methods. The study also revealed that 73% of the reviewed articles primarily focused on addressing challenges related to sustainability, safety and quality, and traceability and transparency. In addition, about 92% of the research contributions originated from European, North American, and Asian geographic countries. Finally, 39% and about 46% of the articles were exploratory by nature and focused on addressing challenges within generic food chains, respectively. Based on a content analysis of the reviewed papers, potential research directions were suggested to fill the identified gaps. The dearth of research focusing on addressing food loss and waste, coordination, globalization, resilience, and robustness, and food-security challenges is one of the identified research gaps. Additionally, the deficiency of empirical studies validating the models/frameworks developed and the meagreness of research focus on unique types of food chains can be addressed as potential research venues.