The program-producing unit of the NBC network produced the first two seasons. When it was cancelled, the show was sold to Columbia Pictures Television for $60 million. Columbia produced the latter two seasons (though there is a one year interval between them) without NBC's involvement.
When the Challenger shuttle, which had history teacher Christa McAuliffe on board, exploded the executives at NBC knew a lot of children would be devastated by her loss as the shuttle launch was shown in many schools. A script was immediately written in which the character of Punky had to come to terms with what the shuttle explosion meant.
Because the show had many young viewers and was scheduled after football games which tended to run overtime, six fifteen-minute episodes were produced. This was done rather than joining a full-length episode in progress, because that would disappoint children watching the program, and showing it later tended to put them up at a time parents may have considered too late for their children.
'Cherie Johnson (I)' was the niece of the show's creator and producer, David W. Duclon, who named the character for her. Nevertheless, she auditioned for the role like everyone else and was picked by the network to play the role.
During the second season, several of the interiors of the set were altered. The beige couch from the first season was replaced with a blue plaid couch. The bathroom and the hallway were altered, and the front door of Henry's apartment was changed as well.
Although not officially an adaptation, Punky Brewster contains many story elements in common with the novel Silas Marner, in which a miserly old hermit whose only friend is an elderly woman adopts a precocious young girl who was abandoned by her parents.