In 1905, Albert Einstein submitted his “annus mirabilis” papers that would change physics forever.
He also submitted his thesis for a doctorate in 1905, and was awarded it that same year by the University of Zurich.
From my understanding he was a patent clerk at this time and even for years before that? How was he able to go from patent clerk to being awarded a PhD so quickly?
A PhD, then and also now in most of Europe, was and is not a planned course of study with exams and coursework; so long as the piece of research you produce is of a high enough standard, you can be awarded a doctorate.
While working at the patent office he was not quite a clerk—he had an advanced technical position that paid him a very good salary. The idea that he was a secretary-type worker is part of the 'mythology' of Einstein, but not quite true. He was in regular correspondence with other physicists (including Alfred Kleiner, who was his doctoral supervisor) during his tenure in the patent office and was working consistently on his theories. He was essentially pursuing his PhD part-time for several years. You can read his thesis online; it's 24 pages long. That may not seem much, but it was enough to constitute an advancement of the field and a contribution to research!