The ninth season of the television series was first broadcast in 2005. The twenty-six episode season was narrated by Michael Angelis in the UK and Michael Brandon in the US.
- 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 Molly make her empty trucks look important.
- Thomas' Milkshake Muddle - Thomas is dismayed when he has to get ingredients to make ice cream.
- Mighty Mac - Mighty Mac is an engine with two faces and 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.
- 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'll 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 causes confusion.
- Thomas' Day Off - Dennis 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 with a ghost story, but Thomas gets back at him.
- Rusty is referred to as female in some American narrations of Tuneful Toots and Duncan and the Old Mine.
- This was Sharon Miller's first season as script editor. Sharon Miller became the first head writer on season 12.
- This was the first season in which Thomas appeared in every episode, albeit not speaking in all of them.