Heat olive oil in a large skillet over medium heat. Add Brussels sprouts and onion; cook and stir until onion starts to turn translucent, about 5 minutes. Stir in garlic, salt, and pepper.
Pour water and gnocchi into the skillet; cover and simmer until water is absorbed and gnocchi are tender, about 10 minutes. Increase heat to medium-high; cook and stir gnocchi until are browned, 2 to 3 minutes. Stir in lemon juice and red pepper flakes.
