The 2016 Mazda Prototype Lites season was the eleventh season of the IMSA Lites championship. The championship featured two classes, L1 and L2. During the season there were few L2 entrants, therefore no championship points were awarded.
| Pos | Driver | SEB | WAT | MOS | TRO | LAG | ATL | Points | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| L1 class | ||||||||||||||||
| 1 |  Clark Toppe | 1 | 2 | 2 | 2 | DNS | 1 | 2 | 1 | 1 | 4 | 2 | 2 | 2 | 2 | 238 |
| 2 | Austin Versteeg | 3 | 1 | 1 | 1 | 1 | 2 | 1 | 6 | 6 | 1 | 13 | 1 | 1 | 1 | 237 |
| 3 | Micheal Whelden | 4 | 3 | 6 | 5 | 3 | 4 | 5 | 8 | 5 | 2 | 1 | 3 | 3 | 11 | 189 |
| 4 | Maxwell Hanratty | 8 | 5 | 3 | 4 | 2 | 5 | 3 | 3 | 2 | DNS | 14 | 4 | 12 | 3 | 166 |
| 5 | Kyle Masson | 5 | 6 | 4 | 3 | 17 | 3 | 16 | 2 | 3 | 3 | 3 | 15 | 13 | 12 | 143 |
| 6 |  James Dayson | 12 | 8 | 10 | 19 | 15 | 6 | 9 | 5 | 4 | 5 | 4 | 12 | 11 | 4 | 111 |
| 7 | Joel Janco | 21 | 15 | 14 | 11 | 11 | 7 | 6 | 9 | 8 | 9 | 8 | 9 | 5 | 7 | 90 |
| 8 | Gerhard Watzinger | 9 | 9 | 11 | 10 | 7 | 10 | 11 | 10 | 11 | 13 | 6 | 6 | 79 | ||
| 9 | Gary Gibson | 20 | 14 | DNS | DNS | 12 | 11 | 7 | 7 | 9 | 6 | 12 | 11 | 4 | 14 | 71 |
| 10 | Brian Alder | 11 | 17 | 13 | 14 | 8 | 9 | 8 | 7 | 7 | 8 | 59 | ||||
| 11 | Michal Chlumecky | 7 | 7 | 5 | 16 | 18 | DSQ | 6 | 7 | DNS | DNS | 50 | ||||
| 12 | Naj Husain | 10 | 12 | 18 | 9 | 16 | 12 | 16 | 6 | 7 | 13 | 43 | ||||
| 13 | Jon Brownson | 13 | 10 | 15 | 16 | 9 | 8 | 17 | 15 | 9 | 10 | DNS | DNS | 39 | ||
| 14 | Dave House | 15 | 18 | 17 | 13 | 18 | 13 | 10 | DNS | DNS | 11 | 10 | 16 | 9 | 8 | 39 |
| 15 |  Andres Gutierrez | 5 | 6 | 4 | 36 | |||||||||||
| 16 | Patricio O'Ward | 2 | 2 | 32 | ||||||||||||
| 17 | Andrew Evans | 8 | 5 | 5 | 32 | |||||||||||
| 18 |  Stuart Rettie | 13 | 12 | 12 | 8 | 5 | 31 | |||||||||
| 19 | Don Yount | 9 | 8 | 6 | 25 | |||||||||||
| 20 | Todd Slusher | 14 | 7 | 8 | 12 | 14 | 25 | |||||||||
| 21 |  Mikhail Goikhberg | 4 | 7 | 23 | ||||||||||||
| 22 | Gerry Kraut | 7 | 20 | 12 | 17 | 10 | 14 | DNS | DNS | 21 | ||||||
| 23 | Andrew Hobbs | 6 | 11 | 15 | ||||||||||||
| 24 | Nathan Blok | 18 | 4 | 14 | ||||||||||||
| 25 | Jay Salmon | 15 | 14 | 15 | 9 | 14 | ||||||||||
| 26 | Chip Romer | 10 | 10 | 12 | ||||||||||||
| 27 | Guy Laporte | 19 | 13 | 17 | 15 | 11 | ||||||||||
| 28 | Tim George Jr. | 19 | 15 | DNS | 13 | 15 | 14 | DNS | DNS | 7 | ||||||
| 29 |  Pedro Cardoso | 18 | DNS | 0 | ||||||||||||
| L2 class | ||||||||||||||||
| Max DeAngelis | 16 | 19 | 14 | 13 | 14 | DNS | ||||||||||
| Jay Salmon | 20 | DNS | DNS | |||||||||||||
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