The third season began airing in early 1993 and was the last season of Shining Time Station.
- Becky Makes a Wish - It seems to be a boring day for Becky at Shining Time Station. But when Mr. Conductor's Wishing Star gets accidentally left behind, hilarity ensues; from Schemer and Stacy swapping places to Midge Smoot having her lips zipped! Will Becky be able to catch the elusive Star, or will the Station fail an important inspection?
- Schemer's Alone - Schemer's Mother is staying overnight in Snarlyville, leaving Schemer to take care of himself for the first time in his life. Instead of taking responsibility, Schemer tries getting everyone to do things for him, and pays his debts with IOU's.
- Bully for Mr. Conductor - With Stacy away to Chubby Corners to help a colleague, Indian Valley Railroad Head J.B. King volunteers to mind the station until her return. He asks Dan and Becky to make his visiting nephew, Buster, feel welcome. Buster turns out to be a bully who targets the smaller Dan and even manages to intimidate Schemer. Mr. King, meanwhile, is distracted from what's going on by his own determined obsession to find Mr. Conductor. Dan is terrified of Buster's threats to beat him up as Mr. Conductor tries his best to make Dan tap into his inner strength to stand up to Buster in order to stop the bullying once and for all.
- Stacy Cleans Up - The abundance of trash at Shining Time Station becomes a problem when the town dump closes. A garbage train driven by Engineer Rusty McRail offers temporarily relief, but ends up aggravating the situation by becoming stranded at the station because all the dumps in the Indian Valley have closed. Becky then comes up with a brilliant idea to eliminate the smelly problem, and in a way inspires the establishment of what could be considered the world's first mobile recycling center on rails!
- Schemer's Robot - Stacy eagerly prepares for the arrival of a new tourist train while Schemer brings in mechanical help to take care of the arcade and do all of his work. While the resulting chaos is going on, we learn that it's Mr. Conductor's turn to man the "Sob Story" booth on the Island of Sodor.
- Billy Saves the Day - Everyone at Shining Time Station is excited, because Felix Perez is organizing a concert. But when he loses his star, everybody (even Schemer!) tries out for the part. Everyone except Billy, for even though he has a great talent, he is afraid to show it. Will a star be founded, or will the concert be cancelled? Find out, as they learn that everyone has something special to offer.
- Billy's Party - It is Thanksgiving and Billy is very busy - he has to repair a locomotive, drive Ginny to buy a turkey, rescue Schemer who has been stranded on a train, and join some very special friends for dinner.
- Fortune Teller Schemer - Everyone thinks that Schemer is a genius when his fortune telling machine correctly predicts the weather, causing him to let his fame go to his head.
- Billy's Runaway Train - Our Shining Time Station friends rehearse and perform a play titled "The Story of Casey Jones," written and directed by Felix Perez. Unfortunately, Billy has to miss the performance due to him being tasked with a freight run to Snarlyville. With Mr. Conductor as his traveling companion, Billy discovers that he can no longer control his train's regulator. With the freight train gaining speed and getting ahead of schedule, Billy realizes that he's heading straight for a disaster unless he gets help.
- Schemer Goes Camping - Everyone goes camping but Schemer neglects to pack most of the important camping equipment.
- Mr. Conductor's Evil Twin - When nobody will help her clean up a mess she made, Kara resurrects Mr. Conductor's Evil Twin and asks him for help. The Evil Twin does help her, but soon creates chaos around the station.
- Bad Luck Day at Shining Time Station - It is Friday the 13th, and Schemer encourages his nephew Schemee to use this occasion to scare people into buying the lucky charms he made. However, Schemee takes his uncle's technique of scaring people a little too far.
- Mr. Conductor's Fourth of July - While people are outside listening to Stacy's speech on freedom, Schemer and Schemee turn the station upside down to look for gold. Schemee vaccuum away Mr. Conductor's magic dust and he can't disappear anymore.
- Stacy Forgets Her Name - Stacy smelled a flower with forgetting dust on it and forgets everything. Schemer sees the occasion to get her to sell the station while Dan and Mr. Conductor help her to remember things again.
- Schemer's Special Club - Schemer begins to "put on airs" when he reveals that the President of the Nickelaire Club, Hobart Hume III, will be coming to visit Shining Time Station. And if he can impress him, he'll let Schemer join the club! But when Mr. Hume arrives, he begins to insult Stacy, Billy and the kids, believing that he's better than all of them. Will Schemer learn sense before it's too late? Find out, as he learns who his real friends are, and laugh when Mr. Hume learns a lesson he'll never forget!
- Mr. Conductor's Movie - When a movie producer arrives, everyone gets excited and wanted to become part of the film. They all went and got costumes hoping to be part of the movie.
- The Joke's on Schemer - The kids tear out a page on a calendar and Schemer thinks that it is April's Fool. He starts making silly jokes and no one understands why he acts like that.
- Dance Crazy - Ginny helps Schemer practice for a dance contest. Dan is shy to dance in front of people because he is afraid that Becky and Kara will tease him.
- Mysterious Stranger - Everyone is scared when things start to disappear in the station. The kids wanted to stay late at the station to catch the thief.
- Dan's Big Race - Dan cannot participate in a bicycle contest because his bike is broken and he hurt his knee. Mr. Conductor cheered him up by telling him stories.
- Mr. Conductor Gets Left Out - The kids watched too much TV and forgot everything else like going to a baseball show, canoe ride and traveling zoo.
- Mr. Conductor's Big Sleepwalk - Mr. Conductor's is asleep when his magic dust went out of control. He wanders around, gets lost and cannot spread his magic dust at night to help everyone sleep.
- The Mayor Runs for Re-Election - It is election time in the town of Shining Time and Mayor Osgood Bob Flopdinger is seeking another term in office. His campaign becomes a disaster when he takes Schemer on as his campaign manager. Things become more complicated for the mayor as a newcomer to Shining Time, Mr. Richhouse, becomes his opponent in the election. Everyone then learns why it is important to vote, and for someone genuine who'll help all the people once elected.
- Stacy Says No - Stacy creates new rules in the station and forgets about her friends. This prevents Dan from playing games and Billy from going fishing.
- How the Station Got Its Name - Kara, Becky and Mr. Conductor went back in time to get a missing part for a lantern. They meet Billy's, Schemer's and Stacy's grandparents.
- Mr. Conductor
- Stacy Jones
- Billy Twofeathers
- Horace Schemer
- Dan Jones
- Kara Cupper
- Midge Smoot
- J.B. King
- Mayor Flopdinger
- Ginny Johnson
- Barton Winslow
- Felix Perez
- Mr. Conductor's Evil Twin
- One Man Band
- Harry Cupper (mentioned)
- Schemer's Mother (mentioned)
- Ted Typo
- Buster King
- Rusty "Rob" McRail
- Doris "Helga" Boonswaddle
- Robby the Robot
- William Twofeathers
- Jebediah Schemer
- B.J. King
- George Carlin as Mr. Conductor and Mr. Conductor's Evil Twin (25/25)
- Didi Conn as Stacy Jones and Gracie Jones (25/25)
- Tom Jackson as Billy Twofeathers and William Twofeathers (17/25)
- Brian O'Connor as Horace Schemer and Jebidiah Schemer (25/25)
- Ari Magder as Dan Jones (21/25)
- Erica Luttrell as Kara Cupper (20/25)
- Danielle Marcot as Becky (25/25)
- Mart Hulswit as J.B. King and B.J. King (11/25)
- Bobo Lewis as Midge Smoot (8/25)
- Jerome Dempsey as Mayor Osgood Bob Flopdinger (3/25)
- Barbara Hamilton as Ginny Johnson (7/25)
- Aurelio Padron as Felix Perez (5/25)
- Gerry Parkes as Barton Winslow (5/25)
- Jonathan Shapiro as Schemee (5/25)
- David Hewlett as Ted Typo (2/25)
- Marium Carvell as a Passenger (1/25)
- Eric Fink as the delivery guy
- Ira Glasner as Buster King
- Jayne Eastwood as Doris "Helga" Boonswaddle
- Michael Polley as Rusty "Rob" McRail
- Elizabeth Hanna as Charles' mother
- Josh Hume as Charles
- Washboard Hank as the One Man Band
- Maurice Dean Witt as Slugger Cobb
- Colin Fox as Hobart Hume III
- Richard Dixon as Mr. Richhouse
- Michael Lamport as Robby the Robot
- Ho Chow as as a tourist
- Larry Reynolds as Older Emmet
- Colin O'Meara as Younger Emmet
The Jukebox Band
- Craig Marin as Rex
- Olga Marin as DiDi
- Jonathan Freeman as Tito Swing
- Kenny Miele as Grace Bass (puppet)
- Peter Baird as Grace Bass (puppet)
- Vaneese Thomas as Grace Bass (voice; uncredited)
- Alan Semok as Tex
- Seven episodes of this season were released on VHS in 1993 and 1994.The episodes that were released were Schemer's Alone, Bully For Mr. Conductor, Mr. Conductor's Evil Twin, Becky Makes A Wish, Stacy Cleans Up, Schemer's Special Club, and Billy's Party.
- Despite the previous season introducing the format of some episodes including one Thomas story instead of two, this is the season that mostly did it for almost every episode.