The fluidic system with an unclogging feature of the preferred embodiment includes a flow channel, a sheath pump to pump sheath fluid from a sheath container into an interrogation zone, and a waste pump to pump waste fluid from the interrogation zone into a waste container. The sheath pump and/or the waste pump draw sample fluid from a sample container into the interrogation zone. The fluidic system also includes a controller to adjust the flow rate of the sample fluid from the sample container into the interrogation zone. The pump and controller cooperate to propagate a pulsation through the flow channel from the pump if the flow channel is clogged. The fluidic system is preferably incorporated into a flow cytometer with a flow cell that includes the interrogation zone.