Don Bluth has said that, if he made the film, he would've made Timmy the villain and Martin the hero. It's unknown if he was joking or if he really meant it.
Don Bluth and his animators were originally chosen to be involved with the sequel as early as 1995. However, due to scheduling conflicts with Anastasia (1997), Metro-Goldwyn-Mayer (MGM) opted to have its in-house animation crew take care of the project.
Arthur Malet and Dom DeLuise were the only actors from the original movie to have reprised their original roles.
In the original Brisby et le secret de NIMH (1982) Timmy has only one line. Here he has the lead role.
Originally going to be a trilogy and was going to make a third film after this. The third film would take elements from the third book "R-T, Margaret, and the Rats of NIMH" in where the rats and mice help two human children Margaret and Artie. However, plans for that sequel were cancelled after the negative reception of this film and Metro-Goldwyn-Mayer Animation was closing their studio when it's founders Paul Sabella and Jonathan Dern left to make SD Entertainment.