Kira's role in the teaser of this episode was written specifically to act as a surrogate for the audience; according to Ronald D. Moore, "It is an absurd premise, and Kira's reaction acknowledges that. It's like a signal to the audience: 'This is kinda silly folks, and we know it's kinda silly, but try to run with us on this one'."
Off screen, this episode was humorously referred to as 'Honey I shrunk the runabout'.
Ira Steven Behr and René Echevarria both wished they had used more comedic characters than the Jem'Hadar. Echevarria later said they should have used the Pakleds, while Behr thought they should have used Harry Mudd.
In an interview with Cinefantastique magazine, Colm Meaney stated that he found One Little Ship (1998) a highlight of the season. He commented: "It gave us a chance to fool around. We love to do comedy. There are some very good comic actors here. Terry is wonderful at comedy and of course Rene is a wonderful comic actor, so we enjoy it."
This episode was nominated for an Emmy Award for Outstanding Special Visual Effects for a Series.