Schaefer is an alternative spelling and cognate for the German word "Schäfer", meaning shepherd, which itself descends from the Old High German scāphare.
"Shaefer", "Schäfer" (a standardized spelling in many German-speaking countries after 1880), the additional alternative spelling "Schäffer", and the anglicised forms "Schaefer", "Schaeffer", "Schaffer", "Shafer", and "Shaffer" are all in common use as surnames.
Read more about Schaefer: Schaefer, Schaeffer, Schäfer, Schaffer, Shafer, Shaffer