A gated photon counting instrument which is capable of operation at the full 100‐MHz repetition rate of mode‐locked ion lasers is described. This instrument provides a high throughput alternative to more complex and costly instrumentation commonly used in time‐correlated single photon counting. Applications to the measurement of subnanosecond fluorescence lifetimes at a 96.8‐MHz laser repetition rate and to the reduction of matrix quenching effects in fluorometry at a 5‐MHz laser rate are presented.