The Family Specials are special episodes made sometime after the third season. As opposed to the original episodes which are half hour, each special goes for an hour.
- Mr. Conductor
- Stacy Jones
- Billy Twofeathers
- Horace Schemer
- J.B. King
- Midge Smoot
- Ginny Johnson
- Dan Jones
- Kara Cupper
- Mayor Flopdinger
- Felix Perez
- Harry Cupper
- Tito Swing
- Grace Bass
- Tex and Rex
- JJ Silvers
- Ned Kincaid
- Ned Kincaid's Great-grandson
- Lilly's Mother
- Kit Twofeathers
- Max Okowsky
- Sister Conductor
- The Queen
- Prince Michael
- The Rat Pack
When Becky made a wish, a cowboy painting on the mural came to life. His name was Ned Kincaid and he became great friends with Stacy Jones. No one knew that Ned Kincaid was just a fictional cowboy coming from the mural from many centuries ago. Schemer became jealous when no one paid attention to him so he decided to start a train full of passengers in order to impress everybody. Suddenly, the train started to move, so Schemer got scared and he jumped out. The train was moving at high speed, but there was no driver. Ned Kincaid came to the rescue and ran after the train on his horse. He managed to jump on the train and save everybody from a big accident. By the end of the day, Ned Kincaid disappeared back into the painting in the mural. That evening, while Stacy was preparing to go home, a man came to the station. To her surprise, the man was very similar to Ned and his family name was also Kincaid!
Billy's nephew Kit came to visit the station. He ran into trouble when he accidentally broke the window of the signal house. Meanwhile, Schemer's baseball team was practicing for an upcoming game. Kit decided to join the team, but he was having a lot of problems hitting the ball and did not felt too good about himself. He had a talk with an old man named Max who gave him some good advice. Max lived alone in the signal house and was a former baseball player. He taught Kit how to play baseball and was a great source of inspiration for the young boy. When Kit was falsely accused of painting on the baseball scoreboard, he felt rejected and decided to leave. However, Max managed to stop Kit's train from departing the station. Meanwhile, Schemer's team was playing against the Snarlyville baseball team. Kit was encouraged to join Schemer's team during the last inning. Thanks to Max's advice, Kit hit a home run to give his team the win. Kit also became good friends with his uncle Billy once again.
Guest stars: Jack Klugman as Max
Mr. Conductor's sister visited him at the station. At the same time, Kara's grandfather Harry also came for a visit. He built a small racing car for Kara and wished that she would participate in the annual race. However, Kara had other plans and didn't want to do everything that Harry wanted her to do. Meanwhile, Mr. Conductor got very upset when his sister used her magic to play tricks on people. During the day of the race, Kara thought about how she had been unfair to Harry. So she decided to participate in the race at the last minute. Unfortunately, the wheel on her car was broken. Sister Conductor decided to help as she and Mr. Conductor flew on a plane and drop a useful tool in Kara's pocket. Kara used the tool to fix her car, and she managed to win the race. At the end, she dedicated the trophy to her grandfather Harry.
As the queen and the prince were traveling on a train, two thieves detached their train coach, thus the royal family accidentally ended up at Shining Time Station. Nobody knew that the queen was a real one. The queen also brought her jewelry in the station, but forgot them when she went to Ginny's house for tea. It was Schemer who found the jewelry and he secretly decided to keep it for himself. Meanwhile, the prince met Becky, Kara, and Kit and became friends with them. He was very happy because he got the chance to hang out with ordinary people, a wish that he always wanted to fulfill. The next day, it was the talent show at Shining Time Station. The kids performed a play, while Schemer showed his singing talents by chanting the song "My Queen!" The two thieves suddenly interrupted the show and began to chase after the queen and Schemer in order to rob the jewels. Schemer and the queen escaped on a motorcycle while the thieves chased them on Ginny's truck. The thieves were later caught and stopped by J.B. King and Stacy Jones.
- George Carlin as Mr. Conductor (4/4)
- Didi Conn as Stacy Jones (4/4)
- Brian O'Connor as Horace Schemer (4/4)
- Tom Jackson as Billy Twofeathers (3/4)
- Ari Magder as Dan Jones (2/4)
- Erica Luttrell as Kara Cupper (4/4)
- Danielle Marcot as Becky (4/4)
- Barbara Hamilton as Ginny Johnson (4/4)
- Bobo Lewis as Midge Smoot (4/4)
- Mart Hulswit as J.B. King (4/4)
- Bucky Hill as Kit Twofeathers (3/4)
- Aurelio Padron as Felix Perez (1/4)
- Jerome Dempsey as Mayor Osgood Bob Flopdinger (1/4)
- Jonathan Shapiro as Schemee (1/4)
Special Guest Stars
- Ed Begley, Jr. as Ned Kincaid and Ned Kincaid's Great-grandson (Once Upon a Time)
- Jack Klugman as Max Okowsky (Second Chances)
- Teri Garr as Sister Conductor (One of the Family)
- Leonard Jackson as Harry Cupper (One of the Family)
- Susan Stackhouse as Lilly's mother (Once Upon a Time)
- Chantellese Kent as Lilly (Once Upon a Time)
- Jeannette Charles as The Queen (Queen for a Day)
- Andrew Sardella as Prince Michael (Queen for a Day)
- Richard McMillan as Biff (Queen for a Day)
- Ron Gabriel as Bull (Queen for a Day)
- Rodger Barton as Bentley (Queen for a Day)
The Jukebox Band
- Craig Marin as Rex and JJ Silvers
- Olga Marin as DiDi
- Jonathan Freeman as Tito Swing
- Alan Semok Tex
- Peter Baird as Grace Bass (puppet)
- Kenny Miele as Grace Bass (puppet)
- Vaneese Thomas as Grace Bass (voice; uncredited)
- Kit Twofeathers joins the main cast in Second Chances.
- Ginny Johnson, Midge Smoot and J.B. King are all main characters in the specials.
- None of the characters mentioned above are listed in the opening credits, however they are listed separately from the recurring characters, like Becky was in the second season.
- This is the first and only Shining Time Station production after season 3 to only feature one specific season of Thomas & Friends (notably season 4).