Preheat the oven to 350°.
Cook the broccoli in 1-inch of water, until almost tender.
Drain, then cook pearl onions in 1-inch of water until almost tender. Drain.
Transfer both to a greased 13x9 inch baking dish.
In a large saucepan, melt ¼ cup of butter. Whisk in the flour, salt, and pepper until smooth.
Gradually whisk in the milk. Bring to a boil, cook and stir until thickened about 1 to 2 minutes.
Reduce the heat, stir in the cream cheese until blended. Add to the vegetables, stir gently to coat.
Sprinkle with the cheddar cheese. Melt the remaining butter, and toss with the bread crumbs. Sprinkle over the bread crumbs.
Bake uncovered, until the topping is golden brown, about 25 to 30 minutes.