This paper verifies the iron loss affected by the secondary frequency in the multi-core transformer for the frequency multiplying circuit. In the frequency multiplying circuit, the secondary frequency component also flows through the primary winding although the transformer is excited by the primary switching frequency, which is one-fifth of the secondary frequency. However, the influence of the secondary frequency to the iron loss of the multi-core transformer in the frequency multiplying circuit has not discussed sufficiently. In this paper, three conditions including a no-load test, a resonant test where the inductance of the secondary side is dominant, and a resonant test where the inductance of the primary side is dominant, are demonstrated in order to verify the influence of the secondary frequency to the exciting voltage and the magnetizing current, that is, the influence of the voltage drop on the primary winding to the iron loss. The iron loss of Mn-Zn ferrite (PC40, TDK) is measured by drawing B (magnetic flux density)-H (magnetic field intensity) curves under the switching frequency is around 200 kHz and the secondary frequency is around 1 MHz. Experimental results verified the increment of the iron loss is 5.1% when the inductance of the secondary side is dominant to the total resonant inductance compared to that in the no-load test. In addition, it is confirmed that the increment of the iron loss is increased by the amplitude of the secondary current. On the other hand, experimental results verified that the secondary frequency significantly affects to the iron loss when the inductance of the primary side is dominant to the total resonant inductance because the voltage drop due to the primary winding's parameters and the secondary frequency component in the primary current occurs. The increment of the iron loss is 35.9% compared to that in a no-load test. From these observations, this paper indicates that placing the resonant inductance at the secondary side is effective for suppressing the influence of the secondary frequency to the iron loss of the multi-core transformer for the frequency multiplying circuit.