A hallmark of cerebral malaria is sequestration of Plasmodium falciparum infected erythrocytes (IE) within the brain microvasculature. Binding of IE to endothelium reduces microvascular flow and combined with an inflammatory response perturbs endothelial barrier function, resulting in breakdown of the blood-brain barrier (BBB). Furthermore, cytoadherence leads to activation of the endothelium and alters a range of cell processes affecting signalling pathways, receptor expression, coagulation, and disruption of BBB integrity. Here, we investigated whether cerebral malaria (CM) derived parasites elicit differential effects on human brain microvascular endothelial cells (HBMECs), as compared to uncomplicated malaria (UM) derived parasites. Patient-derived IE from UM and CM clinical cases, as well as non-binding skeleton-binding protein 1 knockout parasites, were overlaid onto TNF-activated HBMECs in a co-culture system. Gene expression analysis of endothelial responses was performed using Fluidigm probe-based assays of a panel of genes involved in inflammation, apoptosis, endothelial barrier function, and the prostacyclin synthesis pathway. We observed a significant effect on the endothelial transcriptional response in the presence of IE, yet there was no significant correlation between HBMEC responses and the type of clinical syndrome (UM or CM). Further, there was no correlation between HBMEC gene expression and both binding itself and the level of IE binding to HBMEC, as we detected the same change in endothelial responses when employing both binding and non-binding parasites. Our results suggest that interaction of IE with endothelial cells in this co-culture model induce some endothelial responses that are independent of clinical origin and independent of the expression of the major variant antigen PfEMP1 on the IE surface.