Story editor Dennis Spooner edited out much of the humour from the original script as he felt that it was more intellectual; Jones was unhappy with the changes.

Pinfield and the production crew hoped that The Space Museum could be made cheaply to offset more expensive serials, using a small cast and limited sets.

The production crew hoped that The Space Museum could be made cheaply to offset more expensive serials like The Web Planet (1965), doing so with a small cast and few sets, and using Pinfield's technical experience to achieve visual effects without need for excessive filming.

[6] To save on cost, Pinfield used stock music recordings for the incidental score, including pieces from Trevor Duncan, Erik Nordgren, and Eric Siday.

[5] For the second episode, despite being in poor health, Hartnell insisted that Jeremy Bulloch grab him roughly to make the kidnap sequence look authentic.

[11] Maureen O'Brien felt uneasy working with Pinfield due to his old-fashioned approach, feeling that he did not provide sufficient direction to the cast.

The cutaway shots of the main cast standing motionless in display cases were filmed separately; Brian Proudfoot stood in as Hartnell's double, as he had done in The Reign of Terror (1964).

In The Television Companion (1998), David J. Howe and Stephen James Walker considered the first episode promising and the general concept fascinating, but felt that the story "falls as flat as a pancake"; they lauded the main cast, particularly Maureen O'Brien, but criticised the supporting cast, describing Richard Shaw's role as "one of the worst performances yet seen in the series".

[3] In A Critical History of Doctor Who (1999), John Kenneth Muir praised the story's use of two prominent science fiction themes—changing the future, and discovering one's own death and attempting to alter it—comparing it favourably to The Twilight Zone, though he felt that it was diminished by the trope of planetary revolution as previously told in The Daleks and The Web Planet.

[18] In 2009, Mark Braxton of Radio Times felt that the story "kicks off so well", but failed to take the opportunity to discuss ideas such as predestination; he praised Vicki's "vibrant" character, and described the scene of the Doctor in a Dalek casing as "one of the few elements that make this rather tedious traipse memorable".

[16] In 2010, Total Sci-Fi Online's Jonathan Wilkins similarly enjoyed the first episode, but described the remaining three as "dull, bog-standard Who" that "plods rather than races towards a deeply unsatisfactory climax".

[19] SFX's Nick Setchfield enjoyed the "lovely fourth-dimensional weirdness" of the first episode and the "refreshing" Moroks reminiscent of Douglas Adams's work, but ultimately criticised the serial for being a dull representation on the show's formulaic "rebels vs despots" storyline.

[20] Writing for Doctor Who Magazine, Graham Kibble-White said that the first episode falsely set the audience up for "three more weeks of high-concept plotting", which ultimately became "dreary" except for some of Hartnell's charm.

[21] Cliff Chapman of Den of Geek considered the first episode "slow and never really paid-off" and criticised the performances of the guest stars, but lauded the camera direction, effects work, and main cast.

Selected stock music from the serial was included in Space Adventures, a cassette soundtrack compiled by Julian Knott and published by DWAS Reference Department in September 1987, limited to 300 copies; it was re-issued as a CD in October 1998 with some additional material from the story.

[25] The Space Museum was released on VHS in a three-videotape box set by BBC Worldwide in June 1999, alongside the first and third episodes of The Crusade; it also included postcards and a key ring.

The DVD includes audio commentary with William Russell, Maureen O'Brien, Glyn Jones, and Peter Purves, as well as documentaries about the production, the cast's holidays, and Hartnell as told by his granddaughter.