Slice beef into cubes. Assemble 4 long skewers, alternating 5 beef cubes (threaded perpendicular to the cut) with 6 grape tomatoes on each. Arrange skewers in a nonmetallic dish.
In a small bowl, whisk together oil, mustard, vinegar, and thyme. Pour marinade over skewers; turn to coat. Cover and let stand at least 2 hours in the refrigerator, turning periodically.
Heat grill to high and lightly oil grates.
Season skewers with salt and pepper and place them on grill. Cover grill and cook, turning occasionally, until grill marks are visible and meat is cooked to desired doneness, 1 to 2 minutes per side for medium rare.