Preheat oven to 400 degrees F (200 degrees C). Place butternut squash halves cut-side down on a baking sheet. Roast in preheated oven until tender, about 30 minutes. Remove from oven and let cool.
Heat the olive oil in a large pot over medium heat. Add onion and garlic; cook and stir until the onion has softened and turned translucent, about 5 minutes. Stir in roasted butternut squash, vegetable broth, thyme, salt, and pepper.
Bring to a boil; reduce heat to low and simmer for 15 minutes.
Remove from heat and let cool slightly. Carefully transfer soup to a blender or food processor; blend until smooth.
Return soup to pot over low heat until heated through. Serve hot.