So for the past month I've been having a great deal of anxiety over something kind of strange. I've always overthought everything in my life, which led me to wondering whether we as human beings are able to control our thinking. Sometime it seems as if random thoughts pop into my head for no reason at all. For example I could just be at work and randomly think of the upcoming superbowl. However, why did I do that? Did I choose to think about that? Or did the subconcious part of my brain send me that thought? Wondering about this kind of frightens me. I know it's irrational to be scared of it, but it makes me think that we don't really have free will. Do we really control our thoughts? Please answer.

First, let me reassure you that the experience you describe, of having random thoughts pop into your head, is extremely common, and not a sign of anything wrong. (That said, if these occurrences are worrying you, or if the content of the thoughts is disturbing, please consult a mental health practitioner).
As for control: it is consistent with our having some control over our thought processes that there are *also* random or at least non-rational processes that affect us at times.
We know, for example, that concepts, ideas, and images can become linked to each, so that thinking of one thing immediately prompts thought of another. So, for many of us, the word "salt" immediately causes us to think "pepper." Or a few notes of a certain piece of music, or a whiff of a certain fragrance, can stir up particular emotions or memories.
Associations occur as a result of things being frequently paired in our experience, (like the conjunction of the word "salt" with "pepper"), but they can also be built when we have a particularly strong experience -- for example, I was terrified when I saw the film "The Exorcist" and that fear was reawakened for me whenever I heard even the opening notes of the theme music ("Tubular Bells" I think it was called.)
Associations are usually built unconsciously, so they can take us by surprise. There might be something in your working environment that, without your realizing it, was associated in your mind with something to do with the Super Bowl.
Unconscious associations can play a role in our behavior, too. Many people, without knowing it, harbor negative associations with certain racial or ethnic groups -- even if they consciously and sincerely disavow racial prejudice -- and these unconscious or "implicit" biases can affect, in small but important ways, their interactions with members of those racial or ethnic groups.
But the important point, I think, given your question, is that, while we probably cannot eliminate non-rational influences from our thought, we can, in many cases, learn about them and take steps to minimize them. Here's a link to an NPR story about that:

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