Prepare dough by combining masa harina and water in a mixing bowl. Add 1-2 Tbsp water as necessary to ensure the dough is moist. Knead to form smooth dough with a playdough-like consistency. Cover bowl with clean towel and let stand for at least 10 minutes.
Shred zucchini, put in colander, squeeze water out of zucchini and set aside in a bowl.
Mix cheese and salt together. Add cheese to bowl with zucchini and 1/4 cup chopped onion. Put mixture in the fridge to set for 10 minutes.
For each pupusa, with lightly oiled hands, form the "masa" or dough into balls about 2 inches in diameter. Using your thumb, make an indentation into one of the balls, forming a small cup. Fill the cup with about 1 tablespoon of the zucchini, onion, and cheese mixture. Making sure that the filling does not leak, pat the masa together back and forth between your hands to create a flat pancake like dough roughly ¼ inch thick and 4 inches in diameter.
Heat a lightly oiled skillet over medium-high heat. Cook pupusas for 2-3 minutes on each side or until golden brown.