Preheat the oven to 400°F (200°C).
Pat the chicken thighs dry with paper towels. Season both sides with kosher salt and black pepper.
In a food processor, combine the fresh basil leaves, grated Parmesan cheese, pine nuts, and garlic cloves. Pulse until finely chopped.
With the processor running, slowly drizzle in 1/2 cup extra virgin olive oil until the mixture is smooth and emulsified.
Add lemon juice and pulse once to combine. Transfer the pesto to a small bowl.
Heat 2 tablespoons olive oil in a large oven-safe skillet over medium-high heat.
Place the chicken thighs skin-side down in the skillet and sear for 5-6 minutes until the skin is golden brown and crispy.
Flip the chicken thighs and cook for an additional 2 minutes on the other side.
Remove the skillet from heat. Spoon about 2 tablespoons of pesto evenly over each chicken thigh.
Transfer the skillet to the preheated oven and bake for 25-30 minutes, or until the internal temperature of the chicken reaches 165°F (74°C).
Remove from oven and let the chicken rest for 5 minutes before serving.
Serve the baked chicken thighs topped with any remaining pesto.