Not exactly, as the first refers to how frequently you eat hamburgers and the second to the number of them, although that might amount to the same thing. Also, since 'fewer' is a comparative, it implies you have reduced the number of hamburgers (i.e. fewer than before - a time expression would be natural here, like 'I eat fewer hamburgers nowadays').
By the way, in order to avoid ambiguity, it would be better to turn the sentences round:
To keep healthy, I seldom eat hamburgers.
To keep healthy, I eat fewer hamburgers.
Otherwise, it might seem as if the eating of the hamburgers is the health-promoting practice. :)