This disclosure provides a method and system for automated sequencing of vehicles in side-by-side drive-thru configurations via appearance-based classification. According to an exemplary embodiment, an automated sequencing method includes computer-implemented method of automated sequencing of vehicles in a side-by-side drive-thru, the method comprising: a) an image capturing device capturing video of a merge-point area associated with multiple lanes of traffic merging; b) detecting in the video a vehicle as it traverses the merge-point area; c) classifying the detected vehicle associated with traversing the merge-point area as coming from one of the merging lanes; and d) aggregating vehicle classifications performed in step c) to generate a merge sequence of detected vehicles.