The original design of the Wagoneer's rear followed the standard fashion for early 1960's American station-wagons: a slide-down rear glass window (crank-operated standard, electric control optional) with a drop-down tailgate that held the license-plate under a small chrome hood. The roll-down glass was a change from the previous Willys Station-wagon's fold-up rear glass, and provided a less cluttered load area. The Wagoneer would retain the drop-down tailgate throughout its entire production run. Panel trucks differed from the Wagoneer station-wagons by having two side-opening doors.

The taillights were set in flush with the body, and curved around the corner to double as a side-light. The distinctive feature of this taillight design is the surround of a thin strip of chrome, unlike the wider band of chrome on later models. Like the front, the rear bumper was a three-piece design constructed of chromed steel. There was a backward-slanting chrome script "Wagoneer" logo on the side. Though the style of script would change over the years, the three-piece bumper would last through the 1978 model year.

Missing from the above illustration, but visible in this well-worn example of an early Wagoneer, are the optional round bullet-style backup lights found on each side of the tailgate under the taillights. Also note the boxier proportions of the Wagoneer in real-life; automotive advertisement artists often took liberty with the subject-matter of their drawings in order to make them look longer, lower and wider, and the advertisement of the Wagoneer was no exception. Also note the inside-storage location for the spare tire, which was one of two factory-available storage locations. The other place the factory would stow the spare tire was in a drop-down storage area under the body, behind the rear axle.