The Swiss Economic Affairs Ministry (SECO) confirmed that the first transaction by a Swiss drug company had been completed under the Swiss Humanitarian Trade Arrangement (SHTA) created in February.
"The shipment was for a cancer drug used to treat iron overload caused by repeated blood transfusions," spokeswoman Nadine Mathys told AFP in an email.
SECO did not identify which pharmaceutical firm was involved, and gave no details on the size of the shipment.
The system was created to allow Swiss companies in the food, pharmaceutical and medical sectors to send aid to Iran without breaching Washington's sanctions against Tehran.
Iran has faced medical shortages since the US pulled out of a landmark nuclear deal and reimposed tough sanctions in 2018.
Washington exempted humanitarian goods, especially medicines and medical equipment from its sanctions. But international purchases of such supplies are often impossible since international banks refuse to do business with Iran for fear of falling foul of sanctions themselves.
This has sent medicine prices in Iran soaring and has had consequences for people suffering from rare or special diseases that require imported medication.
"The SHTA is progressing," Mathys said Thursday, adding that "a number of companies have already been approved, (and) more companies will follow. Further transactions should be carried out shortly."
An initial pilot transaction was conducted on January 27 after the Swiss government approved the agreement in principle, allowing for payment for the shipment of cancer drugs and medicines needed for organ transplants.