In a large bowl, whisk together the all-purpose flour, whole wheat flour, flaxseed, sugar, chocolate chips, baking powder, and salt.
In a separate bowl, whisk together the eggs, milk, pumpkin, and vanilla until well blended. Pour the liquid ingredients over the dry ingredients and stir until just combined.
Lightly oil or coat a large nonstick skillet or griddle with nonstick cooking spray and heat over medium-high heat. Pour the batter onto the hot skillet using a 1/4-cup measuring cup, forming 4-inch pancakes.
Cook until bubbles begin to appear on the surface of the pancakes and the bottoms turn golden, about 3 minutes. Flip and cook until the other sides are golden, an additional 2 to 3 minutes. Repeat with the remaining cooking spray and batter.