 "Three Words" received mixed to positive reviews from critics. Robert Shearman and Lars Pearson, in their book Wanting to Believe: A Critical Guide to The X-Files, Millennium & The Lone Gunmen, rated the episode five stars out of five, calling it "extremely well-performed by all concerned." Shearman and Pearson felt that the episode was similar to the earlier "Per Manum" and was somewhat formulaic; however, they noted that this was a necessary and positive step towards redefining the series after the changes made in its last two seasons explaining "the point of all this is only to emphasise how different The X-Files universe now feels, the familiarity of the ingredients only making us more aware that the mix is never going to be the same again". Writing for Television Without Pity, Jessica Morgan rated the episode a "B", although she felt that by this stage the series' mythology was moving "in concentric circles of pain and confusion".
