J. cinerea is a deciduous tree growing to 20 m (66 ft) tall, rarely 40 m (130 ft). Butternut is a slow-growing species, and rarely lives longer than 75 years. It has a 40–80 cm (16–31 in) stem diameter, with light gray bark.
The leaves are alternate and pinnate, 40–70 cm (16–28 in) long, with 11–17 leaflets, each leaflet 5–10 cm (2–4 in) long and 3–5 cm (1+1⁄4–2 in) broad. Leaves have a terminal leaflet at the end of the leafstalk and have an odd number of leaflets. The whole leaf is downy-pubescent, and a somewhat brighter, yellower green than many other tree leaves.
Like other members of the family Juglandaceae, butternut's leafout in spring is tied to photoperiod rather than air temperature and occurs when daylight length reaches 14 hours. This can vary by up to a month in the northern and southernmost extents of its range. Leaf drop in fall is early and is initiated when daylight drops to 11 hours. The species is monoecious. Male (staminate) flowers are inconspicuous, yellow-green slender catkins that develop from auxiliary buds and female (pistillate) flowers are short terminal spikes on current year's shoots. Each female flower has a light pink stigma. Flowers of both sexes do not usually mature simultaneously on any individual tree.
The fruit is a lemon-shaped nut, produced in bunches of two to six together; the nut is oblong-ovoid, 3–6 cm (1+1⁄4–2+1⁄4 in) long and 2–4 cm (3⁄4–1+1⁄2 in) broad, surrounded by a green husk before maturity in midautumn.