In a previous paper, Alattas, Grossmann, and Palou-Rivera (2011) developed a single-period, nonlinear programing refinery planning model using the fractionation index (FI) for the crude distillation unit (CDU) equations. In this paper, the single period model is modified to a mixed-integer nonlinear programming (MINLP) model to determine the sequencing, changeovers, and processing times of crude oils over multiple time periods. The MINLP equations include traveling salesman problem constraints to generate the crude oil sequences that maximize profit. Moreover, the disjunction for the fractionation index (FI) is formulated with mixed integer constraints as opposed to the Heaviside function formulation of the previous work. The resulting model is shown to be robust and relatively fast. When subcycles arise, they are eliminated by adding appropriate subtour elimination constraints. Examples with up to 5 crude oils and 6 weeks time horizon are presented to illustrate the application of the proposed model.