During its production, the exterior of the Phantom saw little change; an exception was the modernization of its destination sign (switching from a rollsign to an LED display).

Both TheBus (Honolulu) and Sound Transit Express (for their 2008 Phantoms) had non-opening windows as part of their orders.

As a consequence of using the Phantom chassis, Gillig was also forced to abandon the mid-engine layout offered by the Transit Coach.

For its 1986 introduction, Gillig offered the Phantom School Bus a range of diesel engines, including the Caterpillar 3208 V8 (school buses were largely the only Phantoms with this engine) and the Detroit Diesel 6V92TA (replacing the 6V71 from the Transit Coach).

For school districts with mountainous terrain, the Phantom offered two manual transmission options: the Fuller Roadranger RT6610 and RT11610 10-speeds.

On the forward section of the body, the driver-side windshield was modified, switching from angled to vertically mounted glass.

To give the school bus traffic priority, red warning lights (and amber lights, for Phantom school buses sold outside of California) were fitted in the front and rear roof caps along with a side stop arm.

As the vehicle was to be used for school routes and not for transit use, the rear curbside exit was deleted (a design change also forced by regulations).

As a result, the entry door on the Phantom School Bus was several inches narrower than its mass-transit counterpart.

However, Gillig continued to offer a kneeling feature from the mass-transit Phantom as an option, allowing the driver to lower the front of the bus to curb level when loading/unloading passengers.

Purchased as "gliders" with no powertrain, the buses were fitted with the trolleybus propulsion system from its previous fleet, saving over $20 million from an all-new design.