Preheat the oven to 350ºF. Grease 15 muffin cups with oil or nonstick cooking spray or line with paper liners.
Put the pepitas into a blender and run until they’re the texture of flour, being careful not to overdo it (or you’ll make pumpkin seed butter). Transfer to a large bowl and add the whole wheat pastry flour, brown sugar, baking soda, baking powder, pumpkin pie spice, and salt. Whisk well to combine.
In a medium bowl, whisk together the egg, pumpkin puree, milk, honey, and oil until smooth and combined. Pour over the flour mixture and stir with a rubber spatula just until smooth with no streaks of flour remaining.
Pour the batter into the prepared muffin cups, filling them to ¼-inch shy of the top.
Bake for about 20 minutes, until just firm to the touch and a toothpick inserted in the center comes out clean.
Let cool for a few minutes in the pan, then run a knife around the edge of each muffin and wedge it out of the pan. They are delicate, so be gentle. Allow to finish cooling on the countertop.