Having been here before myself, I think you need to realize what this means for your relationship. You don't feel able to relax and have you-time with her around. This is probably because you place a set of responsibilities on yourself when you spend time with her, but also want to be able to shed those responsibilities at times and do what you're interested in without making her happiness your responsibility from moment to moment.
That's fine, but I think that you also need to remember that one day, if the relationship goes really well, you will live in the same house and share a bedroom. You will not be able to take a day at home away from your relationship with her then, which means that you need to be sure that the nature of your relationship is such that both you and she can share the same space, without feeling under pressure to "act the girl/boyfriend."
So I think it's important to ask yourself what aspects of your relationship stand in the way of you having you-time when she is physically present. Does she not enjoy (or is actively critical of?) your hobbies? If so, then I think you need to modify the dynamics of your relationship so that she understands that your hobby is important to you, and that if the two of you spend enough time together, you are going to spend some of that time doing a hobby she doesn't enjoy, and she can either join you or do something that interests her on her own.
Is she an extrovert (being energized by attention) while you are an introvert (being exhausted by attention?) If so you need to explain this to her. The following comic can be a helpful aid when having this conversation:
Are you placing mental demands on yourself, in her presence, that she doesn't hold you to? If so, then you need to acknowledge that and free yourself of your own expectations that are causing you to not enjoy too much time spent together, for the good of the relationship. Remind yourself that if your putting this pressure on yourself requires time apart, and that hurts her, then the standard you're holding yourself to is actually hindering both of your enjoyment of the relationship.
Ultimately, the key is honesty. Just tell her how you feel. If this is difficult for you, my experience is that if you just tell her that you're sorting out some feelings about your relationship, she will invite you to share them (and genuinely want to hear them.) Most people will surprise you with how appreciative they are of honesty, even when you're being honest about something they dislike. The hurt feelings are temporary, but the trust your honesty builds is long-lasting.
Just be sure that if you explain not just what you want, but why you want it. You're redefining the relationship not because you're not happy with her, but because you want to create a dynamic between the two of you that can work for both of you long term. Let her know that you've been doing things just for her, and need to be allowed to do more for yourself, otherwise you don't think that the relationship can work, and you want to make it work. The changes actually represent a bigger commitment to her, not less of one, even though it means time spent together where you're less attentive toward her. Be sure she understands that.
Some people (especially men) have trouble talking about their feelings, but it's important to weave your feelings into such a conversation. "I feel tired when we spend too much time together. Then I ask for time apart and feel guilty because I don't want to hurt you." Most women, in my experience, really appreciate this because it allows them to feel closer to you. Once they understand the emotions that motivate you, they don't feel that you pulling away is a symptom of emotional distance, just you needing something that they can give you to help the relationship. They will appreciate you being honest about how you feel because it allows them to understand you better and trust you more.
The long-term success of your relationship depends on how well the two of you, working together, can address exactly these types of issues. If you plan to spend your lives together, you will have to be able to communicate how you feel about your relationship, what each of you want, and come up with an effective compromise together. And the longer you wait to have this conversation, the more difficult it will be, because it will feel like more of a departure from your established way of being together.
Source: I did exactly this during a long-term relationship, and have learned from the mistake. When I was with her, I mentally put myself in "boyfriend mode" and after a few days, found myself wanting her to go away so I could just be myself again. In boyfriend mode I wouldn't participate in hobbies that we didn't share together. And I, an introvert, would make a best effort to keep up with her, an extrovert in social situations, which I found genuinely exhausting. It wasn't fair to myself or to her, and deteriorated our relationship in the long run.