Gather and prep produce: cube squash, slice fennel, chop onion, and mince garlic.
Heat oil in a large pot over medium heat.
Soften onion and fennel until translucent, 6–8 minutes, stirring occasionally.
Stir in garlic, thyme, nutmeg, salt, and pepper. Cook until fragrant, about 1 minute.
Add squash and toss to coat with the aromatics.
Pour in broth. Bring to a simmer, cover, and cook until squash is very tender, 20–25 minutes.
Blend soup until silky using an immersion blender. Stir in cream and adjust seasoning.
Melt butter in a skillet over medium heat. Add apple and brown sugar; cook until golden, 5–7 minutes.
Splash in vinegar and toss to glaze. Remove from heat.
Ladle soup into bowls. Top with caramelized apple, fennel fronds, and pumpkin seeds.