文昌鱼科（学名：Branchiostomidae），是头索动物亚门头索纲文昌鱼目之下的一个科。本科几乎囊括大部份物种。

文昌鱼科之下只有一个属：

Branchiostomidae (syn: Branchiostomatidae) is the family that includes most of the lancelets, which are tiny chordates without a true spine but only a flexible notochord.

Almost all lancelets belong to Branchiostoma, the one and only genus in the family Branchiostomidae. The genus was originally going to be called Amphioxus but was later changed to its current name.