Counterexamples can be constructed with the concept of an "ascending HNN extension". The general HNN extension is defined by taking a group $G$, two subgroups $A,B < G$, and an isomorphism $f : A \to B$, choosing a presentation for $G$, and defining $G *_f$ to be the group defined by starting with the presentation for $G$, adding one generator $t$ called the "stable letter", and adding an extra defining relation $t a t^{-1} = f(a)$ for each $a \in A$. One proves that the natural homomorphism $G \mapsto G*_f$ is injective on $G$ and so also on $A$ and $B$.
In the group $G*_f$ it follows that $A$ is conjugate to $B$, because $tAt^{-1}=B$.
So to get a counterexample that disproves your implication, we simply need a group $G$ and two subgroups $A,B$ such that $A$ is isomorphic to one of its own proper subgroups $B < A$. In this situation the HNN extension that one gets by choosing an isomorphism $f : A \to B$ is called an ascending HNN extension.
Perhaps the very easiest example is $G = A = \mathbb Z$ and $B = 2 \mathbb Z$, with isomorphism $f : \mathbb Z \to 2 \mathbb Z$ defined by $f(1)=2$. One obtains the famous Baumslag-Solitar group
$$\langle a,t \mid tat^{-1}=a^2\rangle
$$
in which the infinite cyclic subgroup $\langle a \rangle$ is conjugate to its own index 2 subgroup $\langle a^2 \rangle$.