Upon its release, IBM 1401, A User's Manual received mostly positive reviews from music critics. Pitchfork's Mark Richardson gave it a 6.9, saying that the record "begins beautifully" and has a "powerful finish", "but the long sag in the middle makes IBM 1401 – A User's Manual a bit harder to recommend overall."
Sal Cinquemani for Slant Magazine said that the album "gives you the sense of hearing something truly ancient being married to something very modern and present, and, then, something very futuristic." Cinquemani praised the album's ambition and thematic work while noting that it was less musically varied. "Some theorists claim humans can simulate anything with a computer, even a soul," Cinquemani concluded, "and with IBM 1401 - A User’s Manual, Jóhannsson comes chillingly close."