The forebrain serotonergic system is a crucial component in the control of impulsive behaviours. However, there is no direct evidence for natural serotonin activity during behaviours for delayed rewards as opposed to immediate rewards. Herein we show that serotonin efflux is enhanced while rats perform a task that requires waiting for a delayed reward. We simultaneously measured the levels of serotonin and dopamine in the dorsal raphe nucleus using in vivo microdialysis. Rats performed a sequential food–water navigation task under three reward conditions: immediate, delayed and intermittent. During the delayed reward condition, in which the rat had to wait for up to 4 s at the reward sites, the level of serotonin was significantly higher than that during the immediate reward condition, whereas the level of dopamine did not change significantly. By contrast, during the intermittent reward condition, in which food was given on only about one-third of the site visits, the level of dopamine was lower than that during the immediate reward condition, whereas the level of serotonin did not change significantly. Dopamine efflux, but not serotonin efflux, was positively correlated with reward consumption during the task. There was no reciprocal relationship between serotonin and dopamine. This is the first direct evidence that activation of the serotonergic system occurs specifically in relation to waiting for a delayed reward.