- 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
Half hour format
When Season 9 aired on television, 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.
- Percy and the Oil Painting
- James and the Red Balloon
- Thomas and the Rainbow
- Molly's Special Special
- Edward the Really Useful Engine
- Respect for Gordon
- Thomas and the Toy Shop
- Something Fishy
- Rheneas and the Dinosaur
- Thomas and the New Engine
- Bulgy Rides Again
- Toby Feels Left Out
Night and Day
- Thomas and the Statue
- Toby's Windmill
- Henry and the Flagpole
- Emily Knows Best
- Gordon Takes a Tumble
- Thomas' Day Off
Lost and Found
- Thomas' New Trucks
- Toby Had a Little Lamb
- Duncan And The Old Mine
- Saving Edward
- A Bad Day for Harold
- Thomas and The Golden Eagle
- 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)
- Tiger Moth (cameo)
- Stephen Hatt (cameo)
- Bridget Hatt (cameo)
- The Storyteller (cameo)
- Jeremiah Jobling (cameo)
- The Refreshment Lady (cameo)
- Arthur (music video cameo)
- Elizabeth (music video cameo)
- Jack (music video cameo)
- Alfie (music video cameo)
- Oliver the Excavator (music video cameo)
- Max and Monty (music video cameo)
- Kelly (music video cameo)
- Byron (music video cameo)
- Ned (music video cameo)
- Isobella (music video cameo)
- Patrick (music video cameo)
- Buster (music video cameo)
- Jem Cole (music video cameo)
- Cyril the Fogman (music video cameo)
- Toad (faceless music video cameo)
- 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)
- 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.
- 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.