"Everywhere on Sodor is special, and so are the people and the engines. We are all special!"
-Percy, Percy and the Oil Painting
- Percy and the Oil Painting - Percy takes a fussy painter around Sodor so that he can paint a picture of "The Spirit of Sodor".
- Thomas and the Rainbow - Thomas is distracted by a rainbow.
- Molly's Special Special - Thomas helps new Steamie Molly make her empty trucks look important.
- Thomas' Milkshake Muddle - Thomas is dismayed when he has to get ingredients to make ice cream on a hot day.
- Mighty Mac - Mighty Mac, an engine with two faces, has a problem deciding where to go.
- Thomas and the Toy Shop - Thomas takes some toys to the Knapford toy shop.
- Respect for Gordon - Gordon begins bossing the others about.
- Thomas and the Birthday Picnic - Thomas tries to find a place for Dowager Hatt's birthday picnic.
- Tuneful Toots - Rusty gets stranded while showing the brass band around and uses his horn to save the day.
- Rheneas and the Dinosaur - Rheneas tries to single-handedly take a dinosaur skeleton to the Transfer Yards, much to Skarloey's dismay.
- Thomas and the New Engine - Thomas sees 'Arry and Bert talking to Neville and thinks the three are planning a trick.
- Toby Feels Left Out - A museum is being opened and Toby is worried he will be put in it.
- Thomas Tries His Best - Thomas wants to do something for the fair.
- The Magic Lamp - Peter Sam goes looking for a magic lamp after Skarloey tells him the story of Proteus.
- Thomas and the Statue - Thomas is chosen to take a statue, which he believes is of him.
- Henry and the Flagpole - Henry fears his favourite tree will be cut down to provide a flagpole for Callan Castle.
- Emily Knows Best - Emily pretends to be a queen, only to cause confusion.
- Thomas' Day Off - Dennis the Diesel gets Thomas to do his work.
- Thomas' New Trucks - Thomas is jealous when James gets new trucks.
- Duncan and the Old Mine - Duncan, looking for adventure, ventures into a disused mine.
- Bold and Brave - Diesel tells spooky tales to Thomas and Ben.
- Skarloey the Brave - Skarloey proves to be a daredevil when he tries to ride up the incline.
- Saving Edward - Edward cannot take his train and fears he will be scrapped.
- Thomas and the Golden Eagle - Thomas tries to see a rare golden eagle.
- Keeping Up with James - James' impatience proves to be disastrous.
- Flour Power - Diesel spooks Thomas, but he gets back at him.
- Day and Night
- Party Time
- Every Day's a Special Day on Sodor
- Buffer Up and Share
- Bill and Ben
- 'Arry and Bert
- Peter Sam
- Annie and Clarabel
- Sir Topham Hatt
- Sodor Brass Band
- The Dockyard Manager
- The Ice-Cream Factory Manager
- Dowager Hatt (not named in US narration)
- Lady Hatt (does not speak)
- Farmer McColl (does not speak)
- Henrietta (cameo)
- Caroline (cameo)
- Butch (cameo)
- George (cameo)
- Tiger Moth (cameo)
- Stephen Hatt (cameo)
- Bridget Hatt (cameo)
- The Storyteller (cameo)
- Jeremiah Jobling (cameo)
- Refreshment Lady (cameo)
- Arthur (DVD Game)
- Alicia Botti (learning segment)
- The Tailor (deleted scene cameo)
- Mighty Mac
- Mr. Percival
- The Baker
- The Famous Artist
- Proteus (does not speak)
- The Photographer (does not speak)
Half hour format
When Season 9 aired on PBS Kids, Nick Jr. and Treehouse, it was paired with not just Season 7 episodes, but even some Season 6 episodes which were originally narrated by Alec Baldwin and re-dubbed by Michael Brandon in the US, with Michael Angelis re-dubbing his narrations in the UK. The Season 6 episodes also included the new music as well. In the beginning of the Nick Jr. airings in the UK, an opening when Thomas' crew gets him ready for another days work and an ending when Thomas' crew cleans him after a days work was added.
- Percy and the Oil Painting
- Learning Segment: Who's Under the Coal Dust? - James
- James and the Red Balloon
- Learning Segment: Same Colour
- Thomas and the Rainbow
- Thomas' Milkshake Muddle
- Song: Buffer Up and Share
- Spotless Record
- Learning Segment: Thomas and the Shapes Bridge
- Mighty Mac
- Molly's Special Special
- Learning Segment: Who can get to the Washdown?
- Edward the Really Useful Engine
- Learning Segment: Emily Respects
- Respect for Gordon
- Thomas and the Birthday Picnic
- Song: Party Time!
- Learning Segment: Which Load for What Occasion?
- Harold and the Flying Horse
- Learning Segment: Guess the Engine - Gordon
- Tuneful Toots
- Thomas and the Toy Shop
- Learning Segment: Which Load to Which Station?
- Something Fishy
- Learning Segment: What Route Should Thomas Take?
- Rheneas and the Dinosaur
- Thomas and the New Engine
- Learning Segment: Changing Sounds
- Learning Segment: What's New at the Station
- Bulgy Rides Again
- Learning Segment: Getting to Bluff's Cove
- Toby Feels Left Out
Night and Day
- Thomas Tries his Best
- Song: Day and Night
- Learning Segment: Seeing in the Dark
- No Sleep for Cranky
- Learning Segment: Percy in the Dark
- The Magic Lamp
- Thomas and the Statue
- Learning Segment: What is Thomas Thinking of?
- Toby's Windmill
- Learning Segment: Which Load for Which Route?
- Henry and the Flagpole
- Emily Knows Best
- Song: Pride
- Learning Segment: What Makes Thomas Happy?
- Gordon Takes a Tumble
- Learning Segment: Which Engine with Which Job?
- Thomas' Day Off
Lost and Found
- Thomas' New Trucks
- Learning Segment: Job Destinations
- Toby Had a Little Lamb
- Learning Segment: Dot to Dot - Thomas
- Learning Segment: Where can Neville find Salty?
- Duncan And The Old Mine
- Bold and Brave
- Song: Brave
- Learning Segment: Dot to Dot - James
- Fergus Breaks the Rules
- Learning Segment: Knowing What to do
- Skarloey The Brave
- Saving Edward
- Learning Segment: Fixing the Engines
- A Bad Day for Harold
- Learning Segment: Being Kind
- Thomas and The Golden Eagle
- Keeping Up with James
- Song: Every Day's a Special Day on Sodor
- Learning Segment: What can Cool Down Thomas?
- Edward's Brass Band
- Learning Segment: Cool Down Delivery
- Flour Power
- Rusty was referred to as a female in early American narrations of Tuneful Toots and Duncan and the Old Mine that broadcast on PBS Kids.
- This was Sharon Miller's first season as script editor. Sharon Miller became the first head writer in the twelfth season.
- This was the first season in which Thomas appeared in every episode, albeit not speaking in all of them.
- From this season onward, the title cards are read aloud by the narrator including some of Seasons 6 and 7. However, a few US episodes did not have their titles read aloud in the Thomas and the Toy Workshop US DVD.
- This series saw its terrestrial premiere in 2006, being the first series to air on Channel 5's Milkshake! block. However repeats of Season 8 were shown before.