A system for customized prediction of a menstruation period or a fertility period is provided. The system includes a vital information measurer for measuring vital information about a user, a basic menstruation information generator for calculating the first day of menstruation or an ovulation day using the vital information received from the vital information measurer and outputting the first day of menstruation or the ovulation day as basic menstruation information, a menstruation cycle modeler having a menstruation cycle model representing a menstruation cycle as a function with a predetermined period, and a model parameter estimator for estimating and compensating a menstruation cycle parameter of the menstruation cycle model using the basic menstruation information received from the basic menstruation information generator.