Image encryption is one of the most important techniques to maintain data confidentiality against illegal access and fraudulent usage. In this study, a new medical image encryption technique was developed by combining the discrete wavelet transform, the fast Fourier transform, the Arnold transform, and two multidimensional chaotic systems. The medical image is subjected to a discrete wavelet transform before the magic square shuffles the image sub-bands. Confusion operations are performed on each scrambled subdomain using the Uruk 4D chaotic system. To increase randomness and unpredictability, a second stage of confusion is implemented in the domain of the Fast Fourier transform using the Arnold transform. The final encrypted image is obtained utilizing secret keys derived from the WAM 3D chaotic system. In particular, the initial conditions for chaotic systems are derived from grayscale values, thereby increasing the algorithm’s sensitivity to the input image. The results of the tests and the security analysis indicate that the proposed algorithm is exceptionally reliable and secure.