This article presents the results of a provenance study between late-Neolithic chert artefacts from Malta and chert sources of Sicily. It is part of a larger geoarchaeological research dedicated to investigate whether the cherts used for stone artefacts represent indigenous exploitation or results from longer-distance networks. Chert is a raw material commonly used in prehistory for tool crafting and with abundant geological sources in the broader Mediterranean region. However, the features of most of these sources are unknown and no detailed data regarding their geochemical characteristics and composition are available. The lithic assemblages of late Neolithic Malta are abundant with non-local chert finds and their origin will contribute to inferences about the role of Malta within the broader Mediterranean social landscape and raw-material network of this period. The paper uses macroscopic examination to distinguish the different chert varieties in the assemblages and the non-destructive LA-ICP-MS technique to identify groups with specific geochemical characteristics/signature. The field and lab-based work suggest multiple sources for the chert artefacts and most significantly, presents strong evidence of artefacts having almost identical geochemical signature with specific chert sources from southeast Sicily. These are the first highly reliable results confirming a connection between these two locations and strongly suggests the existence of seafaring in this area during the late Neolithic.