The episode was initially called "Tagged".

Jeri Taylor (executive producer) once described this episode as:
"...a show we weren't entirely sure about in the script stage. [...] We were afraid it was just going to be corny."

Shortly prior to filming the episode, Roxann Dawson (Torres) and Robert Duncan McNeill (Paris) talked for a long time about how the episode explores the relationship between their characters. Dawson told McNeill that, in her interpretation, the reason why their romance was heated to an unusual degree was because it was like the characters were tipsy from having had a couple of drinks that the aliens were supplying, so that the romantic feelings between Paris and B'Elanna were real but were simply being accentuated by the aliens' influence.

Roxann Dawson (Torres) commented on how this episode portrayed the Torres-Janeway relationship:
"It's nice because you see the kind of respect that I've gained for her, and how much it really hurts me to have her be upset with me."

Jeri Taylor (executive producer) voiced her satisfaction with the finished episode:
"'Scientific Method' really came off in production. David Livingston directed it and just did a fantastic job. When I saw it all put together, I was just knocked out, I thought it just had everything. It was very creepy and full of suspense."