Preheat oven to 400 degrees F (200 degrees C). Line a 9x13-inch baking dish with foil.
Place four pieces of bacon in the baking dish and top with walleye fillets. Arrange about 1/4 of the onion slices over the fish. Drizzle with melted butter and honey; sprinkle with salt and pepper. Cover the pan with foil and bake in the preheated oven for until the fish flakes easily with a fork, 12 to 15 minutes.
While the fish is baking, chop up the remaining bacon slices and place them in a skillet with the rest of the onion. Cook and stir over medium heat until the onion has softened and turned translucent, about 5 minutes. Reduce heat to medium-low and continue cooking and stirring until the onion is very tender and golden brown and the bacon is crisp, about 15 minutes more.