Background: Arachnids possess highly specialized and unorthodox sense organs, such as the unique pectines of Scorpiones and the malleoli of Solifugae. While the external morphology, numbers, and shapes of sensory organs are widely used in taxonomic studies, little is known about the internal anatomy of these organs and their associated processing neuropils in the central nervous system. Camel spiders (Solifugae) possess pedipalps and first walking legs heavily endowed with sensory structures, as well as conspicuous malleoli located ventrally on the proximal fourth walking legs. Malleoli are fan-shaped organs that contain tens of thousands of presumptive chemoreceptor neurons, but mechanoreceptive structures are absent. Results: Here, we examine the organization of the synganglion based on microCT analysis, 3D reconstruction of serial paraffin sections, and backfill preparations to trace the malleolar pathway. The projection area of malleolar afferents is intriguingly located in the most anterior ventral nerve cord, located in between the pedipalpal neuromere hemispheres. However, malleolar axon bundles are separated by a thin soma layer that points to an anteriad projection of the fourth walking leg neuromere. A conspicuous projection neuron tract that may receive additional input from pedipalpal sensory organs connects the malleolar neuropil with the mushroom bodies in the protocerebrum. Conclusion: Arthropod chemosensory appendages or organs and primary processing neuropils are typically located in the same segment, which also holds true in Solifugae, although the malleolar neuropil is partially shifted towards the pedipalpal neuromere. A comparison of the malleoli in Solifugae and the pectines in Scorpiones, and of their primary processing neuropils, reveals certain similarities, while striking differences are also evident. Similarities include the ventral arrangement of peg-shaped sensory structures on the respective segmental appendage, exposing dense arrays of chemoreceptive sensilla, and projections to a primary processing neuropil with glomerular subdivision. Differences are, e.g., the lack of mechanoreceptive afferents and an associated processing neuropil.