No. Consider $Y=-I$ and $X=I$.
However, given a real $n$-by-$n$ matrix $X$, the matrix $X^TX$ is positive semidefinite, and every positive semidefinie matrix has a unique positive semidefinite square root.
Let $A$ be a positive semidefinite real $n$-by-$n$ matrix. This means that $A=A^T$ and $x^TAx\geq 0$ for all column vectors $x\in\mathbb R^n$. By the spectral theorem, $A=\sum\limits_{k=1}^m \lambda_k P_k$, where $\{\lambda_k\}_{k=1}^m$ is the set of eigenvalues of $A$, each $P_k$ is a symmetric idempotent, $P_k^2=P_k=P^{T}$, the projection onto the eigenspace for the eigenvalue $\lambda_k$, and $P_kP_j=0$ for $k\neq j$. Because $A$ is postitive semidefinite, $\lambda_k\geq 0$ for all $k$, hence each $\lambda_k$ has a nonnegative real square root $\sqrt{\lambda_k}$. A positive semidefinite square root of $A$ is $\sqrt A=\sum\limits_{k=1}^m\sqrt{\lambda_k}P_k$.
With more work one can show that if $Y^2=A$ and $Y$ is positive semidefinite, then $Y=\sqrt{A}$; this is the uniqueness of positive semi-definite square roots. But there are generally many other square roots if you do not add the condition of positive semidefiniteness.