The vertex set of the Kneser graph $K(n,k)$ is $V = \binom{[n]}{k}$ and two vertices are adjacent if the corresponding sets are disjoint. For any graph $F$, the largest size of a vertex set $U \subseteq V$ such that $K(n,k)[U]$ is $F$-free, was recently determined by Alishahi and Taherkhani, whenever $n$ is large enough compared to $k$ and $F$. In this paper, we determine the second largest size of a vertex set $W \subseteq V$ such that $K(n,k)[W]$ is $F$-free, in the case when $F$ is an even cycle or a complete multi-partite graph. In the latter case, we actually give a more general theorem depending on the chromatic number of $F$. These results generalize the celebrated Erd\H os-Ko-Rado theorem and Hilton-Milner theorem.