This species is characterized by its rather slender habit, thin-textured leaves, flowers borne in sessile small groups along the primary axis, white corollas with tubes 10-14 mm long, white fruits with four ovary locules, and lowland habitat. Gonzalagunia panamensis is the most commonly collected species of the genus in Central America.

Gonzalagunia panamensis is similar in morphology and habitat to Gonzalagunia cornifolia, and these have sometimes been confused; however Gonzalagunia cornifolia has smaller corollas, with tubes 5.5-8 mm long, and is found from Panama through western South America. Gonzalagunia panamensis is also similar to Gonzalagunia ovatifolia, which has even smaller corollas with tubes 2.5-3 mm long. Gonzalagunia panamensis is also frequently confused with the other common species of Central America, Gonzalagunia rosea, which has the flowers borne on short (1-4 mm long) secondary axes, pink corollas, and a habitat in premontane and montane forest. Gonzalagunia panamensis is also similar to Gonzalagunia sagreana, with shorter corollas and 2-locular fruits.