Relapse to alcohol abuse is often caused by exposure to potent alcohol‐associated cues. Therefore, disruption of the cue‐alcohol memory can prevent relapse. It is believed that memories destabilize and become prone for updating upon their reactivation through retrieval and then restabilize within 6 h during a “reconsolidation” process. We recently showed that relapse to cocaine seeking in a place‐conditioning paradigm could be prevented by counterconditioning the cocaine cues with aversive outcomes following cocaine‐memory retrieval. However, to better model addiction‐related behaviors, self‐administration models are necessary. Here, we demonstrate that relapse to alcohol seeking can be prevented by aversive counterconditioning conducted during alcohol‐memory reconsolidation, in the place conditioning and operant self‐administration paradigms, in mice and rats, respectively. We found that the reinstatement of alcohol‐conditioned place preference was abolished only when aversive counterconditioning with water flooding was given shortly after alcohol‐memory retrieval. Furthermore, rats trained to lever press for alcohol showed decreased context‐induced renewal of alcohol‐seeking responding when the lever pressing was punished with foot‐shocks, shortly, but not 6 h, after memory retrieval. These results suggest that aversive counterconditioning can prevent relapse to alcohol seeking only when performed during alcohol‐memory reconsolidation, presumably by updating, or replacing, the alcohol memory with aversive information. Finally, we found that aversive counterconditioning preceded by alcohol‐memory retrieval was characterized by the upregulation of brain‐derived neurotrophic factor (Bdnf) mRNA expression in the medial prefrontal cortex, suggesting that BDNF may play a role in the memory updating process.