Given the growing number of working elderly, monitoring fatigue developing at work is of utmost importance. In this study, 38 participants (18 elderly and 20 young adults) were recruited to perform a prolonged computer task including 240 cycles while their heart rate was measured. In each cycle, the participants memorized a random pattern of connected points then replicated the pattern by clicking on a sequence of points to complete an incomplete version of the pattern. Task performance in each cycle was calculated based on the accuracy and speed in clicking. After each 20 cycles (one segment), participant rated their perceived fatigue on Karolinska Sleepiness Likert scale (KSS). The mean and range of heart rate, HRM and HRR respectively, in each cycle were calculated and together with the performance were averaged across each segment. Statistical analysis revealed that HRR followed an increasing trend in both young and elderly groups as time on task (TOT) increased, p < 0.001. The HRM exhibited a tendency to increase with TOT in both groups, p = 0.063. The performance increased in the elderly group and fluctuated in the young group, p < 0.001. The KSS increased in both groups with TOT, p < 0.001. No interactions between TOT segments and groups were found in any of the measures except in case of performance indicating a higher performance for the young group with a fluctuating temporal pattern. The results provide insights on the feasibility of using heart rate as an index to monitor fatigue in both young and elderly computer users.