Score is a measure of how much a player has achieved in Polytopia. Score is measured in points. In Perfection Mode, players must have the most points to win. In Glory Mode, players need 10,000 points to win. There are various ways of getting points:

- Harvesting Resources: 5 points per population given
- Exploring New tiles: 5 points each
- Upgrading Cities: see Cities
- Spawning Units: (5 * cost) points (Ex: Warrior costs 2 stars, 2 * 5 = 10, so 10 points)
- Parks: 250 points each
- Monuments: 400 points
- Researching technology: (100 * Tier) points (Ex: Research Climbing, a tier 1 tech, 100 * 1 = 100, so 100 points)
- Capturing villages: 100 points
- Level 1 Temples: 100
- Level 2 Temples: 150
- Level 3 Temples: 200
- Level 4 Temples: 250
- Level 5 Temples: 400
- Border Growth: +20 points per new tile in your territory and +5 for every explored tile

In Perfection mode, the map is always 256 squares large. The difficulty bonus multiplier can be seen on the "Game Stats" screen, and is determined as follows:

Easy: 110% for 1 opponent, + 10% per extra opponent (120% for 2 opponents, 130% for 3 opponents, etc) Normal: 130% for 1 opponent, + 10% per extra opponent (140% for 2 opponents, 150% for 3 opponents, etc) Hard: 150% for 1 opponent, + 10% per extra opponent (160% for 2 opponents, 170% for 3 opponents, etc) Crazy: 190% for 1 opponent, + 10% per extra opponent (200% for 2 opponents, 210% for 3 opponents, etc)

Note that you can only choose a number of opponents equal to 3 plus the number of extra tribes you have unlocked.

The difficulty bonus is multiplied by your final score. For example, on an Easy game with 2 opponents (120% difficulty bonus), if you scored 10000 before difficulty multiplier, your final score would be 12000. The same score on a Crazy game with 3 opponents would give you a final score of 21000.