I tried rearranging it and factoring the sum of squares, so that I get
$$xn=(y-x)(y+x)$$
But at this point I have just no clue how to continue. I tried to manipulate the fact that $n$ divides right hand side, but it didn't work at all, so I don't even consider that attempt worth putting there. I also tried playing around with parity and checking the cases, but it also was pointless. So, please, help me with that. I've been trying to solve this problem for the eternity
We can use the discriminant: $ax^2 + bx + c = 0$ has rational solutions iff $D = b^2 - 4ac$ is a perfect square. Let's put $x(x+n) = y^2$ in the form $ax^2 + bx + c = 0$: $$x^2 + nx - y^2 = 0 \text{ has } a = 1, b = n, c = -y^2,$$ therefore integer solutions are only possible when $D = n^2 - 4(1)(-y^2) = n^2 + 4y^2$ is a perfect square.
In such a case, $(n, 2y, \sqrt{D})$ form a Pythagorean triple, and from looking at the parametrization for Pythagorean triples, it is clear that any natural number $n$ other than $1$, $2$, or $4$ can be in a Pythagorean triple $(n, 2y, \sqrt{D})$ for some nonzero integer $y$.
(If $n = 1$ or $n = 2$, then the only possibility for $2y$ is $2y = 0$. $n = 4$ doesn't work because in that case the only nonzero possibility for $2y$ equals $3$.)
Therefore the equation $x(x+n) = y^2$ has positive integer solutions $(x, y)$ for all natural numbers $n$ other than $1, 2, 4$. $\blacksquare$