Through fault current usually refers to fault current that flows through an unfaulted portion of the system to a fault in another location. You need to check that the protection for a certain zone will not trip on through fault current to a downstream zone.
Usually this comes up in bus or transformer differential relaying. The CT signals measuring current at the inlet and outlet of the protected zone are compared by the differential relay to determine if the fault is in or out of the zone. Since fault currents are large, the CT's might saturate and cause false tripping.
Example: A facility is fed by 4000A, 480V switchgear. To reduce arc flash hazard the engineer installs a full bus differential protection system with 4000:5 A CT's on the Main and every feeder breaker. The bus differential relay monitors the currents in and out and trips the Main quickly for a fault in the switchgear. Fault current is 50,000A at a downstream MCC fed by a feeder breaker. For a fault on the MCC bus, through fault current will flow through the Main and the feeder breaker CT?s. Only the feeder breaker should trip on its short circuit protection. The bus differential should not trip the Main Breaker (or any other breaker) because the fault is not in the switchgear. The engineer has to check the CT circuit and relay characteristics at that maximum through fault current to verify that a false trip will not occur due to CT saturation.
