Neem is a fast-growing tree that can reach a height of 15–20 metres (49–66 ft), and rarely 35–40 metres (115–131 ft). It is evergreen, but in severe drought it may shed most or nearly all of its leaves. The branches are wide and spreading. The fairly dense crown is roundish and may reach a diameter of 20–25 metres (66–82 ft). The neem tree is very similar in appearance to its relative, the Chinaberry (Melia azedarach).

The opposite, pinnate leaves are 20–40 centimetres (7.9–15.7 in) long, with 20 to 30 medium to dark green leaflets about 3–8 centimetres (1.2–3.1 in) long. The terminal leaflet often is missing. The petioles are short.

The (white and fragrant) flowers are arranged in more-or-less drooping axillary panicles which are up to 25 centimetres (9.8 in) long. The inflorescences, which branch up to the third degree, bear from 250 to 300 flowers. An individual flower is 5–6 millimetres (0.20–0.24 in) long and 8–11 millimetres (0.31–0.43 in) wide. Protandrous, bisexual flowers and male flowers exist on the same individual tree.

The fruit is a smooth (glabrous), olive-like drupe which varies in shape from elongate oval to nearly roundish, and when ripe is 1.4–2.8 centimetres (0.55–1.10 in) by 1.0–1.5 centimetres (0.39–0.59 in). The fruit skin (exocarp) is thin and the bitter-sweet pulp (mesocarp) is yellowish-white and very fibrous. The mesocarp is 0.3–0.5 centimetres (0.12–0.20 in) thick. The white, hard inner shell (endocarp) of the fruit encloses one, rarely two, or three, elongated seeds (kernels) having a brown seed coat.

The neem tree is often confused with a similar looking tree called bakain. Bakain also has toothed leaflets and similar looking fruit. One difference is that neem leaves are pinnate but bakain leaves are twice- and thrice-pinnate.