Sometimes, current transformers (CTs) are saturated in power systems due to increase of flux passing through the CT core. The distorted CT secondary current can lead to maloperation of protective relays. In this study, a new algorithm is proposed for detection of saturation interval by analysing secondary current signal using variational mode decomposition (VMD). The VMD can decompose signals into different modes which are concentrated around centre frequencies. The start and end points of saturation regions are estimated by using decomposed modes signals. Comprehensive simulations are implemented in PSCAD/EMTDC environment while the main parameters which have direct effect on saturation levels are considered in simulation studies. The performance of the proposed method is evaluated in different conditions: light, moderate, severe and AC CT saturation conditions. The promising obtained results of real data test show that the proposed method can detect the CT saturation time intervals with high accuracy in practical applications.