The indiscrete (= trivial) topology is the only counterexample.
Let $X$ be a connected regular space, and suppose that $X$ is countable. Then $X$ is Lindelöf, and a regular Lindelöf space is normal (though not necessarily $T_1$). If $X$ contains two non-empty disjoint closed sets, Uryson’s lemma ensures the existence of a continuous surjection $f:X\to[0,1]$, showing that $|X|\ge 2^\omega$. Thus, $X$ cannot contain a pair of non-empty disjoint closed sets.
Suppose that $x\in X\setminus F$, where $F$ is a non-empty closed set; by regularity $x$ has an open nbhd $U$ such that $x\in U\subseteq\operatorname{cl}U\subseteq X\setminus F$. But then $\operatorname{cl}U$ and $F$ are non-empty disjoint closed sets, which is impossible. It follows that no non-empty proper subset of $X$ is closed and hence that no non-empty proper subset of $X$ is open. Thus, $X$ must have the indiscrete topology.