Not only does erectile dysfunction (ED) reflect penile vascular disorder in the majority of patients, but it also implicates their high systemic cardiovascular risk. Based on the principle of reactive hyperemia after a brief period of penile ischemia, in this study, we tested the validity of a new Penile Arterial Waveform Analyzer (PAWA) in assessing the relative increase in post-ischemic penile perfusion. Twenty young adult males (mean age 24.24 ± 2.45) without known history of cardiovascular diseases were recruited, whose anthropometric characteristics were recorded and their serum testosterone levels as well as biochemical profiles were determined. A penile cuff was applied to each subject, with cuff pressure being increased from 80 to 250 mmHg, each for 4 min, followed by reperfusion for 7 min. By dividing the area under waveform contour of hyperemic and baseline signals after Ensemble Empirical Mode Decomposition (EEMD), a Penile Perfusion Index (PPI) was calculated. Penile Brachial Index (PBI) was also obtained for comparison. The results not only showed a significant agreement between PPI and serum testosterone levels, but also a superiority of PPI to PBI in distinguishing the high- and low-risk groups for potential ED (PPI: p = 0.039 vs. PBI: p = 0.147). PPI was also demonstrated to show significant correlations with waist circumference (p < 0.001), body mass index (p = 0.005), body weight, total triglyceride, high-density lipoprotein, and systolic and diastolic pressures (all p < 0.05). In conclusion, we proposed a portable and easy-to-operate system in assessing the relative increase in penile perfusion after brief ischemia. The PPI thus obtained correlated significantly with serum testosterone levels as well as key anthropometric and serum biochemical parameters even in apparently healthy young adults, suggesting its potential as a sensitive tool in monitoring penile vascular function and risk for ED.