The serotonergic system has been known to play an important role in acquisition, consolidation and retrieval of memories. Specific serotonin (5-HT) receptor modulation can effectively impact the consolidation of these memories. Determining how specific 5-HT receptor modulation can impact consolidation of spatial memories has been examined, although the 5-HT6 receptor has not been a focus of such studies. The current study aims examine the impact of 5-HT6 receptor agonist EMD386088 administration on the consolidation of a probabilistic spatial discrimination. Female and male C57BL/6 J mice were trained on a probabilistic spatial discrimination then received acute systemic injections of either 0, 1 or 5 mg/kg EMD386088 immediately after reaching learning criterion for the spatial discrimination, targeting the consolidation window. During the retention test, both doses of 1 mg/kg and 5 mg/kg significantly impaired performance in both female and male C57BL/6 J mice. Although there were no significant differences between the two doses, mice treated with either dose of EMD386088 required significantly more trials to reach retention criterion compared to vehicle-treated mice. These learning impairments were independent of effects on locomotor measures due to the comparable trials per min across all treatment groups during both the acquisition and retention tests. The current findings demonstrate the potential sensitivity of treatment timing in the application of novel therapeutics aimed at stimulating 5-HT6 receptors and their impact on memory.