Cook bacon in a large pot over medium heat until browned and crisp. Transfer to a plate lined with a paper towel. Reserve pot.
Add butter and leek to the reserved pot. Cook, stirring occasionally, until just tender, 3 to 4 minutes. Add fennel seeds. Cook, stirring, until fragrant, 1 minute. Add flour and cook, stirring, 1 minute. Slowly whisk in milk and then stock. Add potatoes and thyme. Season with salt and pepper. Bring to a boil, reduce heat, and simmer until potatoes are tender, 20 minutes.
Add chicken and corn. Cook until soup is heated through, 1 to 2 minutes. Discard thyme.
Serve topped with bacon and chives.