Bring stock to a boil in a saucepan on medium-high heat. Add squash, then reduce heat to medium-low and cook for 25 minutes or until squash is tender, stirring occasionally. Puree mixture in a food processor or a blender (let cool for 5 minutes first so that the lid doesn't pop off.).
Meanwhile, cook gnocchi according to directions; drain. Stir gnocchi and milk into squash puree and heat through. Garnish with thyme sprigs.