Bring water to a boil in a saucepan. Add buckwheat; cover. Reduce heat to low; cook until water is absorbed, about 20 minutes. Remove from heat; fluff with a fork.
Melt butter in a skillet over medium heat. Stir in pesto sauce and onion. Cook and stir until onion is tender, about 5 minutes. Add buckwheat; stir to combine. Season with salt and top with Parmesan cheese.