The length of the tail is 112-155mm, the hind foot is 30-36mm, the ear is 14-16mm, and the total length is 221-242mm. The pacific jumping mouse is larger than other members of the genus. The coarse pelage is strongly tricolored. It has a distinct separation of dorsal and ventral colors. The dorsum is dark brown, the sides are dark orange-brown and occasionally flecked with black, the ventrum is mostly white or diffused with dusky brown, and the chest often has a patch of buff that extends to the venter. Its tail is sparsely haired, has guard hairs, and is dark brown above and white below. The ears are fringed with the same color as the dorsum or light brown, and the tip of the ear is spade-shaped. The color of the pelage becomes paler in autumn.
The skull is broad and deep in proportion to length, the pterygoid fossa wide, the zygomatic arch widely bowed, and the mesopterygoid fossae narrow. The mandible has a wide and inflected angle, and the coronoid process is long, slender, and divergent from the condyloid process. The upper incisor is narrow and grooved in front. M1 and M2 have an isolated (free) paracone, and the first primary fold divides the occlusal pattern of M1. The lower M1 lacks an anteromedian fold in the anteroconid.
The dental formula is 1/1 0/0 1/0 3/3.
The posterior of the Pacific jumping mouse's body is heavier than the fore part. Zapus trinotatus is pentadactyl, and the soles of its feet are naked. Its hind legs are much longer than its forelegs. It has a small head which is slightly elongated, and its eyes are small and are located midway between its nose and its ears. The ears are short, but longer than the surrounding fur. There are four pairs of mammae on Z. trinotatus: one inguinal, one abdominal, and two pectoral mammae pairs. There are no cheekpouches.
The pacific jumping mouse has specializations for locomotion. It has well-developed hind legs, lengthened distal elements of hind limbs and digits, a shortened body, a lenthened tail, a shortened neck with increased cervical flexure, posterior shift of its center of gravity, a modified vertebral column to 39 vertebra, a and lengthened pseudosacrum. These traits help Z. trinotatus jump.
(Nowak 1991, Gannon 1988)