Line a baking sheet with paper towels. Cut a thin slice off the top of each tomato. Gently scoop out tomato seeds and pulp, leaving shell intact. Set shells cut side down to drain on paper towels.
Mix tuna, olives, parsley, capers, olive oil, thyme and pepper, breaking up large chunks. Season with salt and additional pepper, if desired.
Spoon tuna mixture into tomatoes and serve.