Fungal infections are a rapidly increasing public health problem due to their high morbidity and mortality rates, especially in populations with compromised immune systems. Rapid and accurate diagnosis of these diseases is, therefore, necessary to improve the prognosis of afflicted patients. Unfortunately, current clinical chemistry practice relies on lengthy culturing methods that are insufficient to meet the fast turnaround requirements. Here we present a cost-effective and robust nucleic acid sensor that can identify the presence of histoplasmosis causing fungal genes, in whole blood or bronchoalveolar lavage (BAL) samples, far earlier than current methods. Our novel assay involves the hybridization of target gene sequences with immobilized nucleic acid probes, allowing direct, label-free detection of Hcp100, CBP1, and M antigen genes through electrochemical analysis. The resultant current is attributed to the presence of fungal targets in the sample solution. The assay provides ultra-sensitive detection of DNA molecules with a limit of detection (LOD) values down to 100 aM, sufficient to meet the clinical diagnostic need. In addition, the turnaround time for the sample to result is less than 90 min compared to the current clinical procedure's turnaround time of 3-4 weeks.