Bring a large pot of salty water to a boil and prepare pasta according to package instructions.
While pasta is cooking, prepare the cheese sauce in a medium saucepot by melting the butter over medium heat. Whisk in the flour, salt, and pepper and cook until flour dissolves into the butter, about 60 seconds, whisking frequently.
Pour in the milk and bring the mixture to a low boil, whisking occasionally.
Add in the shredded cheese and stir until melted; remove from heat.
Drain pasta and return to large pot. Pour in the cheese sauce and stir until pasta is evenly coated.
Stir the peas into the pasta as well as the tuna and heat until warmed through, about 2 minutes.