Intensity modulated radiation therapy (IMRT) is a widely used cancer treatment technique designed to target malignant cells. To enhance its effectiveness on tumors and reduce side effects, radiotherapy plans are usually divided into consecutive treatments, or fractions, that are delivered over multiple weeks. However, typical planning approaches have focused on finding the full sequence of radiation intensities prior to the treatment, or were restricted to a single treatment session. In this work, we investigate a fractioned variant of the IMRT planning problem that accounts for geometric motion-related uncertainty during treatment. We propose a novel multistage stochastic programming (MSP) modeling framework that incorporates the sequential decision-making nature of the problem and prevailing stochasticity in cancer treatment. The model is solved via a sample average approximation based on stochastic dual dynamic programming considering a variety of risk measures. We conduct computational experiments on five test cases that are generated based on clinical data. Through extensive simulations, we show that our MSP model generates higher quality treatment plans compared to deterministic and two-stage program counterparts based on multiple performance measures. In particular, our model leads to a higher rate of tumor coverage and a lower rate of radiation exposure for healthy tissues. Accordingly, the proposed MSP framework can greatly contribute to the clinical practice in fractionated IMRT.