Sepsis requires very sensitive and rapid detection of biomarkers to guide antibiotic therapy to lower the patient mortality rate. Here, we report an ultrasensitive, rapid, and low-cost method for detection of the most popular sepsis biomarker, procalcitonin (PCT), based on a split aptamer-based fiber optic nanogold-linked sorbent assay. After successful development of a novel aptamer for PCT by SELEX, a pair of split aptamer fragments from the parent aptamer was predicted through molecular interaction simulation via free webservers. Then one fragment (AptF1) is modified on a sensor fiber and the other fragment (AptF2) is conjugated to a gold nanoparticle (AuNP@AptF2). The interactions among PCT and the two aptamer fragments lead to the formation of a AuNP@AptF2-PCT-AptF1 sandwich-like nanocomplex on the fiber core surface, leading to strong nanoplasmonic absorption near the fiber core surface. This method provides a linear response ranging from 500 fg/mL to 5.0 ng/mL and a detection limit of 50 fg/mL (3.9 fM). The method had been validated against the clinical accepted electrochemiluminescence immunoassay using clinical samples and very good correlation between the results by both methods was found. Therefore, this method offers a potential for point-of-care diagnosis of sepsis.