In 1991, Heiser joined the School of Computer Science and Engineering of UNSW Sydney, originally as a lecturer, reaching the rank of full professor in 2002, a position he retains to date.

His group produced Mungi, a single address space operating system,[2] for clusters of 64-bit computers, and implementations of the L4 microkernel with very fast inter-process communication.

[4] After joining NICTA at its creation in 2002, his research shifted away from high-end computing platforms, and toward embedded systems, with the aim of improving security, safety, and reliability via use of microkernel technology.

[5] This led to the development of a new microkernel, called seL4, and its formal verification, claimed to be the first-ever complete proof of the functional correctness of a general-purpose OS kernel.

[7] His work on virtual non-uniform memory access (vNUMA) demonstrated a hypervisor which presents a distributed system as a shared-memory multiprocessor as a possible model for many-core chips with large numbers of processor cores.