Methods of beam fluence sequencing for intensity modulated proton therapy (IMPT) using the beam scanning technique are presented. Proton beam weight maps optimized by the treatment planning system (TPS) for a discrete set of regularly spaced narrow pencil beams were interpolated, using convolution with various kernel functions, to simulate continuous beam scanning on a raster pattern. Expected dose distributions at the proton Bragg peak range were then calculated and compared to those planned by the TPS, to evaluate the discrepancy due to the differences between the treatment planning and delivery approaches. An iteratively optimized adjustment was applied to the simulated continuous beam fluence profiles to reduce such discrepancy. Calculation showed that by accounting for the specifics of the scanning method, the planned dose distribution on the target may be reproduced to within 0.5% of the maximum target dose, given the pencil beam spacing smaller or equal to the beam sigma is used for treatment planning. For the beam weight maps generated using a spot spacing larger than sigma, a substantial reduction in the calculated dose discrepancy may be attained by applying an iterative adjustment of fluence profiles obtained by interpolating over artificially expanded set of beam spots.