I have the initial value problem $\left\{\begin{gather}E_nf_n(x)+f_n''(x) = 0\\ f_n(-a)=f_n(a)=0 \end{gather}\right.$.
Solving it using Laplace transform I get $$f_n(x) = f_0\cos(\sqrt{E_n}x)+\frac{f_0'}{\sqrt{E_n}}\sin(\sqrt{E_n}x)$$ In my attempt to solve for $f_0$ and $f_0'$ I did the following
$\left\{\begin{gathered}f_n(a) = f_0\cos(\sqrt{E_n}a)+\frac{f_0'}{\sqrt{E_n}}\sin(\sqrt{E_n}x)=0\\ f_n(-a) = f_0\cos(\sqrt{E_n}a)-\frac{f_0'}{\sqrt{E_n}}\sin(\sqrt{E_n}x)=0\end{gathered}\right.$
Adding and substracting both equations, assuming $f_0 \neq 0$ and $f'_0 \neq 0$, I get $\left\{\begin{gathered}\cos(\sqrt{E_n}a)=0\\ \sin(\sqrt{E_n}a)=0\end{gathered}\right.$ Here I'm a bit lost and dont' know how to proceed further. If I list all the possible solutions for $\cos(\sqrt{E_n}a)=0$ and $\sin(\sqrt{E_n}a)=0$, I can't find $E_n$ such that $\cos(\sqrt{E_n}a)=0$ and $\sin(\sqrt{E_n}a)=0$, the intersection of both sets is the empty set.
How could I proceed into finding a solution for the IVP? I tried to solve it using Mathematica but it gives that $\cos(\sqrt{E_n}a)=0$ or $\sin(\sqrt{E_n}a)=0$, in which case I get a set of values for $E_n$, mainly $E_n = \frac{\pi^2n^2}{4a^2}$. How could I get to this solution with the equations I showed above?
Also, How could I find $f_0$ and $f_0'$? or how could I find a relation betweeen $f_0$ and $f_0'$?

This is a eigenvalue problem, so we are looking for $E_n$ such that the differential equation has nontrivial solutions.
Your choice that both $f_0\neq0$ and $f_0'\neq0$ (at the same time!) is too restrictive. You get solutions by either
This concludes the problem. However we can rewrite both families of solutions solutions into one single family of solutions if we rewrite the cosine functions as shifted sine functions: $$ \cos(\sqrt{E_n^c}x)=\cos(\tfrac{(n+1/2)\pi}{a}x)=(-1)^{n}\sin(\tfrac{(n+1/2)\pi}{a}x+(n+1/2)\pi)=(-1)^{n}\sin(\tfrac{(2n+1)\pi(x+a)}{2a}) $$ If we now define $$E_k=\begin{cases}E_{k/2}^s&k \mbox{ even}\\E_{(k+1)/2}^c&k \mbox{ uneven}\end{cases}$$
and similarly with the functions, we get the result from mathematica.
A potentially easier approach is to consider the shifted problem to begin with: $g(x+a):=f(x)$ which yields the problem: $$ E_ng_n(x)+g''_n(x)=0\\ g_n(0)=g_n(2a)=0 $$
this yields only sine functions as nontrivial solutions directly.