Major shooting was completed in May 2006. It was filmed on location in Bacchus Marsh, Victoria and suburbs in Melbourne, Australia. The fair scene in the story was filmed in Heidelberg in Melbourne, Australia at Heidelberg West Football Club's football ground.
Most of the shooting was done in Victoria, Australia. As it wasn't the correct season in Melbourne during the county fair scenes, the trees surrounding the location were spray painted with non-toxic orange and yellow paint to make it seem as though it was autumn. And, rather than have extras getting motion sickness on the rides, the art department sculpted bodies out of polystyrene and took casts of their own faces that were put onto the dummies. These dummies were painted and dressed up and strapped into rides; going round and around for about a week - and no motion sickness. Each of their faces (about 5 of them) were on all of the 60 or so dummies.
According to the 2007 DVD director's commentary, Templeton's feasting at the fair sequence was expanded after a test audience missed the Sherman Brothers' (Robert B. Sherman and Richard M. Sherman) song, "A Veritable Smorgasbord," they remembered from Charlotte's Web (1973).
The Australian extras in the County Fair scene were told at one point to make some sounds for the microphones to pick up, to sound like real Fair-goers. After one take with their normal accents, they were reminded to be American. Most promptly started just repeating, "Oh my God" and some other modern-day Americanisms.
Visual effects are by Rising Sun Pictures, Fuel International; Proof, Rhythm and Hues Studios; Digital Pictures Iloura, and Tippett Studio. The visual effects supervisor for the film as a whole was John Andrew Berton Jr., who noted that a live action version of Charlotte's Web has become much more practical in recent years due to advances in technology. Winick "was adamant" that Charlotte and Templeton (the film's two entirely computer-generated characters) should be realistic and not stylized, although they did give Charlotte almond-shaped eyes. John Dietz, visual effects supervisor for Rising Sun Pictures, notes that there was a debate over whether to give her a mouth, and that in the end they decided to have her chelicerae move in what he describes as being almost like a veil, as if there were a mouth behind it.
This was the first film based on a book by E.B. White since Stuart Little 2 (2002), which used plot elements directly from the original Stuart Little book. Later entries in the Stuart Little film franchise used wholly original stories.
The statement that the relationship of the Zuckermans to the Arables is not explained in either the book or the previous movie is not exactly accurate. Both state that Homer is Fern's uncle. Since the last names are different, one can logically surmise that Mr. Zukerman is Mrs. Arable's brother.
The film was at one time intended for a June 2006 release, but was pushed back to December 2006 to avoid competition with two other films from Nickelodeon Movies - Nacho Libre (2006) and Barnyard (2006).
The early scenes are identified as in early spring. Wilbur is a spring pig and Fern and her brother are still in school. Yet the corn is thigh high, a height usually achieved by the third week of July.
The song played by the marching band in the county fair is "The Liberty Bell" by John Phillips Sousa. While not the most famous of Sousa's marches, it was also used as the theme music of "Monty Python's Flying Circus." Former Python John Cleese voices Samuel the sheep.