End over end is the same as "head over heels" and "top over tail". The nouns "end" refer respectively (i) to your head or top, and (ii) your heels or tail, as the ends of your body.
(b) head over heels. [...]
(i) With reference to falling, tumbling [=gymnastics], etc.: so that one's heels are in the air and one's head is below them; so as turn completely over, as in a somersault; [to fall, jump or move] headlong. Apparently arising from an inversion of the elements in the earlier phrase "heels over head" and "tail over top."
1987 H. W. Pfanz Gettysburg: Second Day xv. 366 Its [sc. the shell's] burst sent Wilcox's remaining courier..flying head over heels.
2005 K. Hancock Shadow over Kiriath 355 He tumbled head over heels as if bowled toward shore by a powerful wave, then came suddenly upright and still.
Both end over end and head over heels usually refer to travelling a distance whilst falling in a quick and uncontrolled manner.