Abstract Permutation matrices form an important computational building block frequently used in various fields including, e.g., communications, information security, and data processing. Optical implementation of permutation operators with relatively large number of input–output interconnections based on power-efficient, fast, and compact platforms is highly desirable. Here, we present diffractive optical networks engineered through deep learning to all-optically perform permutation operations that can scale to hundreds of thousands of interconnections between an input and an output field-of-view using passive transmissive layers that are individually structured at the wavelength scale. Our findings indicate that the capacity of the diffractive optical network in approximating a given permutation operation increases proportional to the number of diffractive layers and trainable transmission elements in the system. Such deeper diffractive network designs can pose practical challenges in terms of physical alignment and output diffraction efficiency of the system. We addressed these challenges by designing misalignment tolerant diffractive designs that can all-optically perform arbitrarily selected permutation operations, and experimentally demonstrated, for the first time, a diffractive permutation network that operates at THz part of the spectrum. Diffractive permutation networks might find various applications in, e.g., security, image encryption, and data processing, along with telecommunications; especially with the carrier frequencies in wireless communications approaching THz-bands, the presented diffractive permutation networks can potentially serve as channel routing and interconnection panels in wireless networks.