Reubens, 50, who is free on $20,000 bail, entered the plea through his attorney, Blair Berk.
Berk said she would seek to have the charge thrown out at a Jan. 3 pretrial hearing. She also complained to court Commissioner Kristi Lousteau that the city attorney's office had not turned over its evidence to the defense.
"From the day the search warrant was executed I have requested of the Los Angeles Police Department and any prosecuting authority to inform the defense the basis on which the people are proceeding this case," Berk said.
Deputy City Attorney Richard Katz countered that prosecutors were not required to do so until after the arraignment. The prosecution did turn over documents to the defense after the arraignment, but neither side disclosed the contents.
The misdemeanor charge of possessing materials depicting children engaged in sexual conduct stems from a search of the actor's home in November 2001. It carries a maximum penalty of one year in county jail and a $2,500 fine.
In 1991, Reubens pleaded no contest to an indecent exposure charge after his arrest in Sarasota, Fla., for allegedly exposing himself in a movie theater.
While the arrest caused him considerable embarrassment, and cost him his job as the host of a program primarily aimed at children, many people in show business rallied behind him and made it possible for his career to continue.
Roles since his star turn on Pee-wee's Playhouse include parts in the large screen movies "Batman Returns," "The Nightmare Before Christmas," "Matilda," "Doctor Doolittle," and "Blow," and on television, "Buffy the Vampire Slayer," "Hercules" and "You Don't Know Jack." He's also in "Mayor of Sunset Strip," set to be released next year, playing himself.