A frequency controller for operating a switching power converter is provided. The frequency controller includes an output circuit, an operation signal generator, and a transition signal generator. The output circuit is to connect to a switching power converter. The startup signal generator is connected to the output circuit via a first connection line and configured to generate a startup signal with a startup-frequency during a startup period of the switching power converter. The operation signal generator is connected to the output circuit via a second connection line and configured to generate an operation signal with an operation-frequency during an operation period of the switching power converter. The transition signal generator is connected to the output circuit via a third connection line and configured to generate a transition signal with varied frequencies during a transition period between the startup period and the operation period.