The present disclosure pertains to a method and system configured for cough synchronization in a mechanical insufflation-exsufflation system. The system is configured to synchronize (712) the transition from an insufflation mode to an exsufflation mode to a patient initiated cough by detecting cough effort of the patient e.g. at the end of the insufflation phase. The detection of cough effort of the patient is based on one or more parameters associated with gas in the system. Upon detecting that the patient is initiating a cough, the system automatically switches the insufflation mode to the exsufflation mode to assist the patient to generate an effective cough.