Weigh or lightly spoon flour into a dry measuring cup; level with a knife.
Combine flour, thyme, and salt, stirring with a whisk.
Combine milk and eggs in a medium bowl, stirring with a whisk until blended; let stand 30 minutes. Gradually add flour mixture to milk mixture, stirring well with a whisk. Stir in melted butter.
Coat 8 popover cups with cooking spray; sprinkle cheese evenly among cups.
Place cups in oven at 375 for 5 minutes. Divide batter evenly among prepared cups.