Sear the beef short ribs in a large pot over medium-high heat until browned on all sides (about 5-7 minutes). Remove and set aside.

In the same pot, add sliced onions and reduce heat to medium. Cook until caramelized (20-25 minutes), stirring occasionally.

Return seared short ribs to the pot with caramelized onions. Add beef broth, thyme leaves, and balsamic vinegar. Bring to a boil, then simmer for about an hour.

Remove short ribs, shred the meat off the bones, discard bones, and return meat to the broth.

Ladle soup into bowls, top with shredded Gruyère cheese, and broil for about 5 minutes until bubbly and golden.