Caries-affected dentin is covered with a thicker and organically enriched smear layer than normal dentin. This may affect the demineralization ability and the infiltration of self-etch adhesives, thus reducing the efficacy of bonding to caries-affected dentin. This study evaluated the adhesion of a two-step self-etching adhesive to normal and caries-affected dentin after pretreatment with mildly acidic hypochlorous acid (HOCl) solutions. We used a microtensile bond strength (μTBS) test to compare the μTBS of Clearfil SE Bond to either caries-affected dentin or to normal dentin, after pretreatment for 5 s with one of three solutions (806 mM NaOCl, or 0.95 or 1.91 mM HOCl). The μTBS of the self-etch adhesive was significantly lower to caries-affected dentin than to normal dentin. Pretreatment with 0.95 mM HOCl improved the μTBS of the self-etch adhesive to caries-affected dentin, but there was no significant difference compared with normal dentin. On the other hand, pretreatment with 806 mM NaOCl or 1.91 mM HOCl did not demonstrate a significant improvement in the μTBS to caries-affected dentin. None of the pretreatments demonstrated a negative effect on adhesion to normal dentin.