Electrical events in neurons occur on the order of milliseconds, but the brain can process and reproduce intervals millions of times longer. We present what we believe to be the first neuronal mechanism for timing intervals longer than a few seconds. The activation and gradual relaxation of calcium-independent CaMKII measure a 6-min time window to coordinate two male-specific events during Drosophila mating: sperm transfer and a simultaneous decrease in motivation. We localize these functions to four neurons whose electrical activity is necessary only to report the conclusion of the decline in CaMKII's activity, not for the measurement of the interval. The computation of elapsed time is therefore largely invisible to standard methods of monitoring neuronal activity. Its broad conservation, ubiquitous expression, and tunable duration of activity suggest that CaMKII may time a wide variety of behavioral and cognitive processes.