Put oven rack just below middle position and put baking pan on rack, then preheat oven to 450°F.
Trim and peel kohlrabi, then cut into 3/4-inch pieces. Toss kohlrabi with 1 tablespoon oil, 1 teaspoon thyme, 1/4 teaspoon salt, and 3/4 teaspoon pepper in a bowl. Transfer kohlrabi to preheated pan in oven and roast 15 minutes.
Meanwhile, peel butternut squash, then quarter lengthwise, seed, and cut into 3/4-inch pieces. Toss squash with remaining 1 tablespoon oil, 1 teaspoon thyme, 1/4 teaspoon salt, and 3/4 teaspoon pepper in same bowl.
Stir kohlrabi, turning it, then push it to one side of pan.
Add squash to opposite side of pan and roast, stirring and turning squash over halfway through roasting, until vegetables are tender and lightly browned, about 30 minutes total (after squash is added).
Toss vegetables to combine and transfer to a dish.