The sixteenth season of the television series aired during February and March 2012 in the UK and between April and September in the US. The twentieth episode did not air in the UK until Christmas Day 2012.
- Race to the Rescue - Flynn is able to run on the roads again, but he is nervous because his wheels wobble.
- Ol' Wheezy Wobbles - Ol' Wheezy has stopped working. The Logging Locos do not know what to do, but Thomas is sure he can help.
- Express Coming Through - Dowager Hatt is having a party for some very important visitors.
- Percy and the Monster of Brendam - Percy believes one of Salty's tales and looks for "the monster of Brendam".
- Ho Ho Snowman - Charlie hides behind a snowman and tricks Henry into thinking it is alive.
- Flash Bang Wallop! - A photographer wants to take some pictures of the engines for a book.
- Thomas and the Rubbish Train/Thomas and the Garbage Train - Thomas helps Whiff pull a train to the waste dump.
- Thomas Toots the Crows - Thomas tries to keep the crows off Farmer McColl's seeds.
- Bust My Buffers! - Gordon's bufferbeam is broken and he is given a Diesel's bufferbeam.
- Percy and the Calliope - Percy tries to save a calliope from the Smelter's Yard.
- Thomas and the Sounds of Sodor - Thomas helps a great composer look for inspiration.
- Salty's Surprise - Edward tries to find Salty a Christmas present.
- Sodor Surprise Day - Thomas tries to get Gordon to have fun on Sodor Surprise Day, but ruins the fireworks.
- Emily's Winter Party Special - Emily thinks she will be chosen to pull the present train if she finds Sir Topham Hatt's hat.
- Muddy Matters - James needs to travel on muddy tracks to get Farmer McColl's sheep to the fair, but does not want to dirty his paintwork.
- Whiff's Wish - Whiff wishes that he was as grand as Spencer.
- Welcome Stafford - Spencer shows Stafford, the new electric shunting engine, around Sodor, but ignores Victor's warning that Stafford's batteries could run out.
- Don't Bother Victor! - The Thin Controller leaves Peter Sam in charge of the narrow gauge railway.
- Happy Birthday Sir! - Thomas and Winston, the new track inspection vehicle, look for an open-top carriage for the Fat Controller's birthday.
- The Christmas Tree Express - Toby gets scared when he takes Rheneas to Misty Island to pick out a Christmas tree.
- Bash and Dash
- 'Arry and Bert
- Sir Handel
- Peter Sam
- Ol' Wheezy
- Sir Topham Hatt
- Dowager Hatt
- Mr. Percival
- The Duke and Duchess of Boxford
- The Mayor of Sodor
- Farmer McColl
- Farmer Trotter
- The Docks Manager
- The Photographer
- A Tree Specialist
- The Great Composer
- Some Children
- Stanley (does not speak)
- Scruff (does not speak)
- Annie and Clarabel (do not speak)
- Harold (does not speak)
- Captain (does not speak)
- Lady Hatt (does not speak)
- City of Truro (cameo)
- Hiro (cameo)
- Belle (cameo)
- Norman (cameo)
- Paxton (cameo)
- Henrietta (cameo)
- Owen (cameo)
- Merrick (cameo)
- Alicia Botti (cameo)
- Bridget Hatt (cameo)
- Jem Cole (cameo)
- Sodor Brass Band (cameo)
- The Engineer (cameo)
- The Fireman (cameo)
- The Bargeman (cameo)
- Mr. Bubbles (cameo)
- The Two Bakers (cameo)
- The Teacher (cameo)
- The Bird Watcher (cameo)
- The Railway Inspector (cameo)
- Sodor United Football Team (cameo)
- The Railway Coal Inspector (cameo)
- The Small Boy (cameo)
- Dowager Hatt's Friends (cameo)
- Duncan (mentioned)
- Michael Brandon as the narrator and Diesel
- Martin Sherman as Thomas and Percy
- Kerry Shale as Henry, Gordon, James, Bash, 'Arry, Kevin, and Sir Topham Hatt
- William Hope as Edward, Toby, Whiff, Dash, Farmer McColl, Farmer Trotter, Bert and the Duke of Boxford
- Jules de Jongh as Emily, Rosie, Mavis, the Duchess of Boxford, and the Schoolboy
- Ben Small as Charlie and Rheneas
- Keith Wickham as Salty, Den, Stafford, Skarloey, Sir Handel, and Dowager Hatt
- Matt Wilkinson as Winston and Rusty
- Rupert Degas as Dart, Flynn, and Bertie
- Glenn Wrage as Spencer, Ferdinand, Rocky, Butch, and Cranky
- David Bedella as Victor
- Steven Kynman as Peter Sam
UK and AUS
- Michael Angelis as the narrator
- Ben Small as Thomas, Toby, Ferdinand, and Rheneas
- Keith Wickham as Edward, Henry, Gordon, James, Percy, Whiff, Dash, Salty, Den, Stafford, Skarloey, Sir Handel, Sir Topham Hatt, Dowager Hatt, Mr. Percival, the Mayor of Sodor, the Photographer (Flash Bang Wallop!), the Great Composer, and the Man at the Fire
- Matt Wilkinson as Charlie, Bash, Victor, Rusty, Butch, Winston, Rocky, Cranky, Kevin, the Duke of Boxford, Farmer McColl, Farmer Trotter, the Photographer (Muddy Matters), and the Docks Manager
- Teresa Gallagher as Emily, Rosie, Mavis, the Duchess of Boxford, and the Schoolboy
- Rupert Degas as Dart, Flynn, and Bertie
- Steven Kynman as Peter Sam (uncredited)
- Kerry Shale as Diesel and 'Arry
- William Hope as Bert
- This was Sharon Miller's last season as head writer.
- This was the last season animated by Nitrogen Studios.
- Skarloey, Rheneas and Peter Sam's whistles now budge up and down when they use them.
- From this season onwards, the end credits only list the cast members who provide voices in that particular episode. The only exceptions are Whiff's Wish, where Ben Small is incorrectly added to the list of voice actors, and Don't Bother Victor, where Steven Kynman is not credited.
- This is the last season narrated by Michael Brandon and Michael Angelis for the US and UK, respectively.
- This was the last season to have two separate narrators for the UK and US.
- This is the last season to have twenty episodes.