| 1 | Paramount Fanfare / Main Title | Danny Elfman | 1:32 |
| 2 | The Girl on the Flying Trapeze | Danny Elfman | 2:03 |
| 3 | Pee-wee Flies / Happy House / Pee-wee Herman Had a Farm | [traditional] | 1:40 |
| 4 | Rise ’n Shine | Danny Elfman | 2:58 |
| 5 | The Greenhouse / Date Book #1, 2 & 3 | Danny Elfman | 1:00 |
| 6 | Sneaky Walk / Race to School | Danny Elfman | 1:04 |
| 7 | Paparazzi / Winnie’s Hair / Mud / Race to the Store | Danny Elfman | 0:53 |
| 8 | The Big Storm | Danny Elfman | 1:42 |
| 9 | After the Storm / Pee-wee to the Rescue / Lion Problems | Danny Elfman | 1:52 |
| 10 | Where’s Midge? / Lion Tag | Danny Elfman | 0:31 |
| 11 | Circus Parade | Danny Elfman | 0:56 |
| 12 | Sad Drive Home | Danny Elfman | 1:15 |
| 13 | Circus in the House | Danny Elfman | 1:19 |
| 14 | Zsa Zsa / Happy Circus | Danny Elfman | 1:31 |
| 15 | Zsa Zsa’s Delight / Pee-wee’s Inspiration / Hot Dog Tree / Mace’s Inspiration / Pee-wee’s Flower | Danny Elfman | 1:38 |
| 16 | Elephant Ride | Danny Elfman | 1:02 |
| 17 | Idyll | Danny Elfman | 0:46 |
| 18 | Clouds | Danny Elfman | 1:06 |
| 19 | The Big Kiss (film version) | Danny Elfman | 2:31 |
| 20 | Rejection | Danny Elfman | 0:45 |
| 21 | Mace’s Speech / Busy Circus / Square Dance | Danny Elfman | 2:30 |
| 22 | Man to Man / Psycho Winnie | Danny Elfman | 1:20 |
| 23 | Winnie and the Italians | Danny Elfman | 0:33 |
| 24 | Rimprovero | [traditional] | 1:03 |
| 25 | I Llove You | Danny Elfman | 0:32 |
| 26 | Pee-wee Tries / Elephant / Pee-wee Tries Again / Town Spies | Danny Elfman | 3:34 |
| 27 | The Side Show | Danny Elfman | 1:28 |
| 28 | Pee-wee’s Love Theme | Danny Elfman | 2:41 |
| 29 | Shrinking Weenies / Big Top | Danny Elfman | 0:51 |
| 30 | Angry Mob/The Show’s Off / Idea | Danny Elfman | 1:12 |
| 31 | Transformation | Danny Elfman | 1:07 |
| 32 | Big Top Finale | Pee-wee Herman | 3:21 |
| 33 | Pee-wee’s Big Surprise | Danny Elfman | 2:24 |
| 34 | End Credits | Danny Elfman | 3:02 |
| 35 | Idyll (alternate) | Danny Elfman | 0:45 |
| 36 | The Big Kiss (album version) | Danny Elfman | 2:31 |
| 37 | Big Top Finale (instrumental) | Danny Elfman | 3:23 |
| 38 | Pee-wee’s Big Surprise (alternate) | Danny Elfman | 2:26 |
| 39 | The Girl on the Flying Trapeze (instrumental) | Danny Elfman | 2:06 |