Yes, you can say "Thank you, too." when someone says "Thank you." to you. It is a polite and gracious way to acknowledge their thanks while also expressing your appreciation for whatever prompted their gratitude.
For example:
Person A: "Thank you for helping me with the project." Person B: "Thank you, too. It was a team effort."
By responding with "Thank you, too," you are reciprocating their gratitude and showing that you also appreciate their involvement or whatever they did that led to their expression of thanks. It's a friendly and considerate way to continue the positive exchange.