Near infrared autofluorescence (NIRAF) optical coherence tomography (OCT) is an intravascular imaging modality, based on a catheter which emits light at two different wavelengths through an optical fiber. Since OCT is becoming the method of choice in interventional cardiology and NIRAF is proven to be higher in plaque lesions having higher risk morphologic phenotypes, the NIRAF-OCT can become powerful and promising technology. However, there is NIRAF- distance dependence which has to be addressed before the technology can be applied in clinical practice. The present paper aims at presenting a method which calibrates the distance dependent NIRAF signal and ensures that similar NIRAF values are depicted when targeting the same lesion. Towards this purpose, autofluorescence phantoms were constructed, accurate distance measurements were conducted and the NIRAF-distance relationship was quantified. Finally, a calibration function was proposed which is able to accurately calibrate the NIRAF signal in any NIRAF-OCT pullback.