Current radiological evaluation of multiple sclerosis is mainly based on new T2 lesions and active gadolinium enhancing lesions on magnetic resonance imaging (MRI), which only partly identify the pathophysiological processes in MS. Positron Emission Tomography (PET) is an imaging technique that can visualise distinct molecular processes in vivo, and as such provides a unique insight into the pathophysiology of MS. PET imaging of neuroinflammation in MS has focussed on the various receptors upregulated on different microglia phenotypes, as the dynamic and complex process of microglia activation is the hallmark of neuroinflammation in MS. To date, the most important PET marker for neuroinflammation is the 18kDa-translocator protein (TSPO), upregulated on the mitochondria of microglia. Although in general results have been positive and the second generation TSPO tracers have improved the signal-to-noise ratio and increased the bioavailability in the brain, there are still several limitations: the rs6971 polymorphism determining genetic binding affinity, binding sites that are not specific to microglia and the inability to differentiate between the different microglial phenotypes. Therefore, new PET targets for neuroinflammation have been developed. Currently two tracers have successfully been evaluated in MS patients: the adenosine A2A-receptor tracer [11C]TMSX and the purinergic P2X7-receptor tracer [11C]SMW139. Besides the challenges of tracer development, progress in the field of PET research in MS has been hindered by a lack of consensus on suitable analysis methods. Kinetic modelling using arterial input functions provides a method for accurate quantification of specific tracer binding, but arterial sampling limits widespread applicability of PET. Reference tissue methods have been proposed as an alternative, but the diffuse neuroinflammation in MS and the disruption of the blood-brain barrier violate the assumptions underlying such models. Addressing both the tracer development challenges and the modelling challenges specific to MS, will help progress PET imaging from the field of research to a clinical relevant biomarker of neuroinflammation in MS.