A system and method is provided for magnetic resonance imaging (MRI) guided respiratory gated radiotherapy using a respiratory motion model. MRI-guided respiratory gating is performed with a continuously updated model that represents a patient's internal anatomy as a mathematical function of an external respiratory surrogate. The motion model may be built and updated by acquiring images of a tissue in a subject and measuring, using the images, a position of the tissue in the images to determine motion of the tissue. The surrogate respiratory signal is acquired contemporaneously with acquiring the images. Motion of the tissue and the surrogate respiratory signal are correlated to create the motion model for the subject and gating a radiotherapy system may then be based upon the motion model. A multi-planar model-based respiratory gating may also be performed by sequentially imaging a stack of adjacent slice positions.