Preheat the oven to 425 degrees F. Line a baking sheet with parchment paper.
Combine the butter, miso paste, maple syrup, soy sauce, rice wine vinegar, sesame seeds and crushed red pepper in a small saucepan over medium heat. Cook, whisking, until melted and syrupy, about 5 minutes.
Toss the carrots, parsnips and fennel with the miso mixture in a large bowl and sprinkle with salt and pepper. Transfer to the prepared baking sheet and spread in an even layer. Bake until the vegetables are tender and caramelized, 35 to 40 minutes.