"Schroedinger equation" unfortunately is a bit ambiguous word. It could refer to $$i\hbar\frac{d \psi(t)}{dt} = H_t\psi(t) \tag{1}$$
but also to a more precise form like this:
$$ i\hbar\frac{d \psi(t)}{dt} = \left(-\frac{1}{2m}{\bf P}^2 + V_t\right)\psi(t) \:.$$
The former version does not depend on the quantum physical system you are dealing with. So, in particular, it holds for relativistic quantum systems, provided you insert the appropriate Hamiltonian operator therein. If you are studying the quantized Klein Gordon field, there is a corresponding Hilbert space and a corresponding Hamiltonian operator for the quantum states of that system.
In a more abstract version (1) can be used to define the evolution operator of the theory. Assuming $$\psi_t = U(t,t_0) \psi_{t_0} \tag{2}$$ where now there are no restrictions on the used vectors, since the domain of $U(t.t_0)$ is the whole Hilbert space, differently form the domain of $H_t$ which is only a dense subspace in general. Indeed, inserting (2) in (1) and exploiting the fact that $\psi_{t_0}$ is arbitrary, we obtain the equation for $U(t,t_0)$:
$$-i\hbar\frac{d}{dt}U(t,t_0) = H_t U(t,t_0) \tag{3}$$
that at least formally, gives rise to the Heisenberg picture version of Dayson's series as the solution:
$$U(t,t_0) = T\left[ e^{-\frac{i}{\hbar} \int_{t_0}^t H_\tau d\tau}\right]\:,$$
(in QFT is more appropriate to deal with the so called interaction picture so that the in the analogue of (3) uses the only interaction part of the Hamiltonian operators appears in place of $H_t$).
In QFT (at least referring to the non-interacting case) you have to make a distinction between two levels: one-particle situation and arbitrarily many particles case associated with the quantum field.
Let us focus on the former case. There is the Hilbert space ${\cal H}$ of a single particle, for instance that of a scalar boson field $\phi$ verifying Klein-Gordon equation. The Hilbert space is again $L^2(R^3, d^3x)$ position representation or, equivalently, $L^2(R^3, d^3p)$ momentum representation, and there are some other natural representations, for instance the momentum representation but using a covariant measure $dp^3/p_0$. The relation between momentum and position representation is more complicated (one should use the so called Newton-Wigner representation of position observable) and usually is not discussed in textbooks.
Dealing with Schroedinger picture in a fixed inertial reference frame, time evolution for a single particle is always described by the abstract Schroedinger equation (1), where now (I henceforth assume $c= \hbar=1$ for the sake of simplicity):
$$K := P_0 =\sqrt{{\bf P}^2 + m^2I}\:,$$
where $m$ is the mass of the particle and ${\bf P}$ the 3-momentum operator.
A quantized quantum field, however, involves states including an arbitrary number of particles. So one has to pass from the one-particle Hilbert space to the whole Hilbert space of the (free) theory which is called (symmetrized in the boson case) Fock space:
$${\cal F}_+({\cal H}) = C \oplus{\cal H} \oplus ({\cal H} \otimes {\cal H})_s \oplus ({\cal H} \otimes {\cal H} \otimes {\cal H})_s \oplus ({\cal H} \otimes {\cal H}\otimes{\cal H} \otimes {\cal H})_s \oplus \cdots$$
Above $_s$ indicates that one has only to consider the completely symmetric subspace of ${\cal H}\otimes \cdots \otimes {\cal H}$, and $\oplus$ is the ortogonal direct sum of Hilbert spaces. For instance, the vectors in $({\cal H} \otimes {\cal H})_s$ are those describing a system of two identical particles associated with the quantum field.
The Hamiltonian operator of the complete system of particles is therefore given by the sum of the Hamiltonian operators of each subsystem:
$$H = 0 \oplus K \oplus (K\otimes I + I \otimes K) \oplus \cdots $$
In this juncture, the quantum field $\hat{\phi}(t,x)$ is pictured in terms of certain operators working between (arbitrary) couples of subspaces ${\cal H}\otimes \cdots \otimes {\cal H}$, adding and removing particles. I will not enter into details because I should introduce too many notions. I just say that the (Hamiltonian) evolution equation of the quantum field operator constructed this way is, again, given by the Hamiltonian $H$ introduced above:
$$\frac{\partial}{\partial t} \hat{\phi}(t,x) = i[ H, \hat{\phi}(t,x)]\:.$$
That is nothing but the standard evolution equation in Heisenberg picture for any quantum observable. Just a final comment is worth. Writing that equation in terms of $\hat{\phi}$ and its conjugated momentum $\hat{\pi}$, and adding the analogous equation of motion for the latter, one obtains a system of equations that is completely equivalent to the Lagrangian equations of motion for the field, I mean Klein-Gordon equation.