Partial answer:
An odd length cycle (say length $2k+1$) squares to a cycle of the same length; while an even length cycle (say length $2k$) squares to two disjoint $k$ cycles. As Matt Samuel points out, one can find the square root of an odd length cycle, as an odd length cycle with the same length and using the same cycle elements. Thus in order for permutation $S$ to have a square root, when written in disjoint cycle notation, $S$ must have pairs of even length cycles that are the same length, and any number of odd length cycles.
For example, if we wanted a square root of $S=(1,2,3,4,5)(6,7,8,9)(10,11,12,13)$ we could take
$R=(1,4,2,5,3)(6,10,7,11,8,12,9,13)$, and we'd have $R^2=R\circ R=S$.