Enterprise-wide optimization for the petroleum refining industry involves optimization of the supply chain involving manufacturing and distribution with emphasis on integration of the different decision making levels. The key manufacturing operations include crude oil loading and unloading, mixing of crude oil, production unit operations of conversion and separation, operations of blending, and distribution of products. Other components of the petroleum supply chain network include oil explorations, crude oil procurement, and sales and distribution of products. The main issues present in the petroleum industry across various decision levels (strategic, tactical, and operational) and within oil refinery operations are discussed. This paper presents an extensive literature review of methodologies for addressing scheduling, planning, and supply chain management of oil refinery operations. An attempt is also made to identify the future challenges in efficiently solving these problems.