There is the whole derivation of it but I'll be discussing a brief overview.
This is for the perspective projection where the line joining the eye and the center of the projection/image plane is perpendicular to it. Like here

As we can easily see, by similar triangles $\triangle ABC$ and $\triangle AEF$ we have
$Y_p / Y = D/-Z$
where $Y_p$ is the projected $Y$ coordinate on to the image plane. $AB = D$ is the total distance from eye to the image plane and is usually set to 1.
Hence we have,
$Y_p = (Y*D)/-Z$
Most APIs also set that the camera is facing towards the negative Z axis following the convention for right handed coordinate system, hence the negative sign. The projection plane is also assumed to be a rectangle instead of a square. It's 2 units long in the $Y$ direction and centered at the origin i.e in the range [-1,1] so it's 1 unit long in the positive Y axis and 1 unit long in the negative. However horizontally, its in the range $[-A, A]$ so when calculating $X_p$ we have to correct for this factor.
$A = Width\ of\ rectangle/Height\ of\ rectangle$
Similarly for $X_p$ and $Z_p$ we have,
$A*X_p = (X*D)/(-Z)$
$X_p = (X*D)/(-Z*A)$
$Z_p = D$
We can easily see see that
$tan(Y_{fov}/2) = BC/D = 1/D$
$D = 1/tan(Y_{fov}/2)$
Here, $Y_{fov}$ is the angle of field of view in the Y axis. Since we are only talking about the upper half its $Y_{fov}/2$.
Hence one way to write $X_p$ and $Y_p$ is
$X_p = \frac{X}{-Z} * \frac{1}{A*tan(Y_{fov}/2)}$
$Y_p = \frac{Y}{-Z} * \frac{1}{tan(Y_{fov}/2)}$
This is what you are seeing in the matrix. The $X$ and $Y$ come from the vector at which the transformation matrix is applied and the $-Z$ term is accounted for by the $-1$ in the 4th row. This $-Z$ is stored as the $w$ coordinate which is then used in perspective division in which we divide by $w$.
For more information you can check this site here
Note:- Haven't discussed properly about NDC space, perspective divide and about near and far planes in $Z_p$ as that would take too much time. Just wanted to show you that it can be derived.