Yes. See Lemma 1 in this answer, which says that it is sufficient to prove
$$\iint_{R_1\times R_2} F(x, y)\, dxdy=0$$
for any pair $R_1, R_2$ of rectangles in $\mathbb{R}^n$. Now the characteristic function $\chi_{R_1\times R_2}(x, y)$ factors out as $\chi_{R_1}(x)\chi_{R_2}(y)$ and it can be approximated by a product $g(x)h(y)$ where $g, h\in C^\infty_c(\mathbb{R}^n)$ (see Lemma 2 of the aforementioned answer for details on this).
P.S.: I just noticed that we could equally use the Fourier transform approach by Zarrax. Let $\phi, \psi\in C^{\infty}_c(\mathbb{R}^n)$ be arbitrary and note that
\begin{equation}
\begin{split}\mathcal{F}\big[F(x,y)\phi(x)\psi(y)\big]_{(x,y)\to(\xi, \eta)}(\xi, \eta)&=\iint_{\mathbb{R}^n\times\mathbb{R}^n}F(x, y)\left(\phi(x)e^{-ix\cdot\xi}\right)\left(\psi(y)e^{-iy\cdot\eta}\right)\, dxdy\\
&=0
\end{split}
\end{equation}
by assumption. Therefore the function $F(x,y)\phi(x)\psi(y)$ vanishes, and since $\phi$ and $\psi$ were arbitrary, we can conclude that $F(x, y)$ vanishes at almost all $(x, y)\in\mathbb{R}^n\times\mathbb{R}^n$.