Bring a large pot of salted water to a boil over medium heat and add the broccoli. Blanch until tender-crisp and bright green, about 3 minutes. Drain well and set aside.
Melt the butter in a large skillet over medium heat. Add the shallots, garlic, and pecans, and saute until the shallots and garlic are tender, about 3 to 4 minutes. Season with salt and pepper, to taste. Keep stirring until the butter begins to brown, another 3 minutes. Add the red pepper flakes and the broccoli. Using tongs, toss the broccoli with the butter and pecans. Cook, while tossing, until the broccoli is heated through, about 5 to 6 more minutes. Remove from heat and transfer to a serving bowl. Sprinkle with the lemon juice and season with salt and pepper, to taste.