Let $G=F\ast_\varphi t$ be an HNN extension of a free group $F$ with two equal associated normal subgroups $H_1 = H_2$ of finite index. We prove that the word problem in $G$ is decidable in polynomial time. This result extends to the case where the subgroups $H_1=H_2$ are not normal, provided that the isomorphism $\varphi:H_1\to H_2$ satisfies an additional condition described in Section 5.