The thirteenth season of the television series aired in January and February 2010 in the UK and began airing in the US in September of 2010. From this season onwards, all footage was CGI-animated.
Michael Angelis and Michael Brandon narrated all twenty episodes, but, like Hero of the Rails, voice actors provided the voices for the characters.
- Creaky Cranky - Cranky teases Thomas about being small, but when he breaks down it's up to Thomas to save him.
- The Lion of Sodor - Thomas has to deliver The Lion of Sodor to Knapford, but, thinking that it is a real lion, he tries to feed it.
- Tickled Pink - James is sent to the Steamworks to be repainted, but needs to leave suddenly, in a pink undercoat.
- Double Trouble - Thomas takes Sir Topham Hatt to his birthday party or does he?
- Slippy Sodor - Thomas is teased about his "funny funnel" and causes trouble for Sir Topham Hatt and Mr. Bubbles.
- The Early Bird - While Percy is at the Steamworks for repairs, Thomas must pull the mail, but he doesn't want to ask for his advice.
- Play Time - Charlie, the new engine, challenges Thomas to race him around the island, causing Thomas to neglect his job.
- Thomas and the Pigs - Thomas is to bring straw to Farmer Trotter's Pig Farm for the piglets who are soon to be born, but Thomas thinks they'll like other things better.
- Time For a Story - After ignoring warning signs about track repair, Thomas' trucks of books derail, so he brings the children to the books.
- Percy's Parcel - After Percy ruins Dowager Hatt's birthday parcel, he hides in a siding. But when he overhears Mavis he gets an idea how to fix his mistake.
- Toby's New Whistle - Toby's bell needs repairs, so he is given a very loud whistle while it's being mended.
- A Blooming Mess - Emily thinks that Mavis needs to be cheered up, so she brings her some flowers, but winds up causing confusion and delay.
- Thomas and the Runaway Kite - After Stephen and Bridget Hatt's kite flies away, Thomas tries to catch it, but realises that he needs to ask for help.
- Steamy Sodor - When Thomas is put in charge of the Steamworks havoc ensues.
- Splish, Splash, Splosh! - Thomas and Rosie play "Splish, Splash, Splosh", but when Thomas splashes Sir Topham Hatt and Alicia Botti he must put things right.
- The Biggest Present of All - Hiro is visiting Sodor, and the Fat Controller is planning a welcome party for him. Thomas is told to tell the other engines, but looks for a present for Hiro instead.
- Snow Tracks - Gordon is told to not go up any hills, but when he does, he creates a giant snowball.
- Henry's Good Deeds - Henry attempts to help people but ends up scaring away the Sodor Warbler, a very famous bird.
- Buzzy Bees - Thomas' special of bees escape when he goes by a flowery meadow. So he takes Hiro's flower truck to try to lure them back to their hive.
- Hiro Helps Out - Hiro gives the engines orders when he thinks the Fat Controller is too busy to do it himself.
UK and AUS
- Michael Angelis as the narrator
- Ben Small as Thomas and Toby
- Keith Wickham as Percy, James, Gordon, Henry, Edward, the Fat Controller, Dowager Hatt, Sir Lowham Hatt, the Mayor of Sodor, and Mr. Bubbles
- Teresa Gallagher as Emily, Mavis, Rosie, Lady Hatt, Bridget Hatt and her friends, and the teacher
- Togo Igawa as Hiro
- Matt Wilkinson as Spencer, Rocky, Victor, Kevin, Cranky, Charlie, Stephen Hatt, the Knapford stationmaster, the Maithwaite stationmaster, Farmer Trotter, the bird watcher, and Farmer McColl
- Jules de Jongh as Alicia Botti
- Kerry Shale as Diesel
- Michael Brandon as the narrator, Diesel, Mr. Bubbles, and the Maithwaite Stationmaster
- Martin Sherman as Thomas and Percy
- Kerry Shale as Sir Topham Hatt, Henry, Gordon, James, Kevin, and Sir Lowham Hatt
- William Hope as Edward, Toby, Stephen Hatt, Farmer McColl, and Farmer Trotter
- Glenn Wrage as Spencer, Rocky, and Cranky
- Jules de Jongh as Emily, Mavis, Rosie, Bridget Hatt and her friends, Alicia Botti, and the teacher
- Togo Igawa as Hiro
- David Bedella as Victor
- Keith Wickham as Dowager Hatt
- Ben Small as Charlie
- This is the first season to exclusively use CGI.
- From now on all episodes are 10 minutes long, instead of 7.
- The episodes, "Splish, Splash, Splosh!", "Playtime", "Slippy Sodor", and "Snow Tracks" were seen in select US theatres in November 2009.
- "Thomas and the Runaway Kite", "Buzzy Bees", "Toby's New Whistle", and "The Biggest Present of All" were shown in select US theatres in January 2010.
- "The Lion of Sodor", "Thomas and the Pigs", "Time For a Story", and "Hiro Helps Out" were shown in select US theatres in October 2010.
- This was the second season not to feature the Skarloey Railway and its engines since their introduction, the first being season 8.
- Thomas was the main character in 13 out of 20 episodes, making this the most "Thomas-themed" season.
- Several characters were left out of this season due to the CGI switch over.
- Thomas' whistle now budges up and down every time he blows it.
- Edward was the only Steam Team member to not have a leading role in an episode.
- Harold and Trevor also appear in CGI during the Sodor Island intro.
- The Sodor Island intro is not used at the start of UK broadcasts from this season onwards.