Abdominal aortic aneurysm (AAA) is a bulge in the abdominal aorta and cause high mortality and morbidity due to the unbalanced condition with haemostasis. AAA has been found with the diameter of 5.5 cm/lager needs a surgical treatment; otherwise, it ruptures with the excessive bleeding. Aneurysm infiltrating macrophage is located in the site of damaged tissue and actively expresses matrix metalloproteinase-9 (MMP-9). MMP-9 is highly correlated with increasing diameter of aneurysm. This research work was designed to detect MMP-9 level on interdigitated electrode (IDE) sensing system to identify the condition of AAA. Specifically, selected aptamer against MMP-9 was utilized as the probe to detect MMP-9 on IDE. MMP-9 detection was enhanced by modifying the surface of IDE with multiwalled carbon nanotube conjugated aptamer through the amine linker. On the linear range between 1 and 60 pM, the limit of detection was at 2 pM with the linear regression (y = 0.2579x + 0.0246; R2 = 0.9477). In addition, spiking of MMP-9 in human serum did not interfere the detection with the IDE designed.