Given two positive integers $n\geq 3$ and $t\leq n$, the permutations $σ,π\in \operatorname{Sym}(n)$ are $t$-setwise intersecting if they agree (setwise) on a $t$-subset of $\{1,2,\ldots,n\}$. A family $\mathcal{F} \subset \operatorname{Sym}(n)$ is $t$-setwise intersecting if any two permutations of $\mathcal{F}$ are $t$-setwise intersecting. Ellis [Journal of Combinatorial Theory, Series A, 119(4), 825--849, 2012] conjectured that if $t\leq n$ and $\mathcal{F} \subset \operatorname{Sym}(n)$ is a $t$-setwise intersecting family, then $|\mathcal{F}|\leq t!(n-t)!$ and equality holds only if $\mathcal{F}$ is a coset of a setwise stablizer of a $t$-subset of $\{1,2,\ldots,n\}$. In this paper, we prove that if $n\geq 11$ and $\mathcal{F}$ is $3$-setwise intersecting, then $|\mathcal{F}|\leq 6(n-3)!$. Moreover, we prove that the characteristic vector of a $3$-setwise intersecting family of maximum size lies in the sum of the eigenspaces induced by the permutation module of $\operatorname{Sym}(n)$ acting on the $3$-subsets of $\{1,2,\ldots,n\}$.