Toll like receptor 9 (TLR9) is an innate immune receptor important for recognizing DNA, both of host and foreign origin. A mechanism proposed to prevent excessive response to host DNA is the requirement for proteolytic cleavage of TLR9 in endosomes to generate a mature form of the receptor (TLR9471-1032). We previously described another cleavage event in the juxtamembrane region of the ectodomain that generated a dominant negative form of TLR9. Thus, there are at least two independent cleavage events that regulate TLR9. Here we investigated whether an N-terminal fragment of TLR9 could be responsible for regulation of the mature- or negative regulatory-form. We show that TLR9471-1032, corresponding to the proteolytically cleaved form, does not function on its own. Furthermore, activity is not rescued by co-expression of the N-terminal fragment (TLR91-440), inclusion of the hinge region (TLR9441-1032) or overexpression of UNC93B1, the latter of which is critical for trafficking and cleavage of TLR9. TLR91-440 co-immunoprecipitates with full-length TLR9 and TLR9471-1032, but does not rescue the native glycosylation pattern, thus inappropriate trafficking likely explains why TLR9471-1032 is nonfunctional. Lastly, we show that TLR9471-1032 is also a dominant negative regulator of TLR9 signaling. Together these data provide a new perspective on the complexity of TLR9 regulation by proteolytic cleavage and offer potential ways to inhibit activity through this receptor, which may dampen autoimmune inflammation.