In this paper, we study the level-set of the zero-average Gaussian Free Field on a uniform random $d$-regular graph above an arbitrary level $h\in (-\infty, h_{\star})$, where $h_{\star}$ is the level-set percolation threshold of the GFF on the $d$-regular tree $\mathbb{T}_d$. We prove that w.h.p as the number $n$ of vertices diverges, the GFF has a unique giant connected component $\mathcal{C}_1^{(n)}$ of size $η(h) n+o(n)$, where $η(h)$ is the probability that the root percolates in the corresponding GFF level-set on $\mathbb{T}_d$. This gives a positive answer to the conjecture of \cite{ACregulgraphs} for most regular graphs. We also prove that the second largest component has size $Θ(\log n)$. Moreover, we show that $\mathcal{C}_1^{(n)}$ shares the following similarities with the giant component of the supercritical Erdős-Rényi random graph. First, the diameter and the typical distance between vertices are $Θ(\log n)$. Second, the $2$-core and the kernel encompass a given positive proportion of the vertices. Third, the local structure is a branching process conditioned to survive, namely the level-set percolation cluster of the root in $\mathbb{T}_d$ (in the Erdős-Rényi case, it is known to be a Galton-Watson tree with a Poisson distribution for the offspring).