Preheat the oven to 375 degrees F (190 degrees C). Spray a 9x13-inch baking dish with nonstick spray.

Season flounder fillets on both sides with salt. Place into the prepared baking dish and brush with 1 tablespoon lemon juice.

Mix Parmesan, melted butter, mayonnaise, green onions, and remaining 2 tablespoons lemon juice together in a bowl. Spoon mixture over fillets.

Bake in the preheated oven for 10 minutes. Turn on the broiler and broil until fillets are just browned on top, 3 to 5 minutes.