EMMA is a 20 MeV non-scaling fixed field alternating gradient accelerator (NS-FFAG) currently under construction at Daresbury Laboratory. NS-FFAGs are a new type of accelerator that offer the prospect of smaller, cheaper accelerators operating at high frequency and with a high duty cycle. They will have a major impact on the design of next generation clinical accelerators for proton and carbon ion treatment of cancers. EMMA will demonstrate the practical application of NS-FFAG acceleration using electrons injected from the ALICE energy recovery linac. The control system for EMMA will reuse much of the infrastructure already in place for ALICE which was built as an EPICS system using PPC CPUs, VME and VxWorks. While maintaining a high degree of compatibility, the EMMA control system will make increased use of low-cost EPICS IOCs based on 1U rack-mounting PCs running Linux, embedded LabVIEW control and a new suite of user interface software using a .NET Channel Access library and controls. Device control and interlock protection will be provided by an in-house designed CAN Bus system that is currently being further developed to include additional analogue input capability.