Can I connect an indoor timer to lights split to 3 circuit breakers?
Either 3 timers, one on each circuit, or one timer, controlling 3 relays, one relay on each circuit. The timer and relay control can be on a 4th circuit, or on one of the three circuits if there is capacity available.

Whatever device does the switching needs to be adequate to handle switching the load - that is, the relay contacts must be rated to carry as much (or more) current and voltage as is being switched on. One advantage of using relays is that the timer contact only needs to be sized for controlling the relay coils, generally a much smaller load.