Add the shallots; cook, stirring frequently, until lightly browned (about 5 minutes).
Add in 1 3/4 cups water, the orange zest and juice, vinegar, and sugar; season with salt and pepper.
Bring to a boil; cook over medium heat until most of the liquid has evaporated, the shallots are tender enough to be easily pierced with a knife tip, and the remaining liquid is syrupy (35-40 minutes).
You may need to increase the heat to high if the shallots are tender but not yet glazed.