Objectives To assess the rate of Influenza Like Illness (ILI) among influenza vaccinated and non-vaccinated employees on rate of absenteeism and presenteeism due to ILI, and to estimate the cost benefit of influenza vaccination in workplace from the employer’s perspective. Methods A cross-sectional questionnaire survey was conducted amongst employees of a private hospital voluntarily vaccinated, were compared with non-vaccinated employees matched for age, sex, and job category. The outcome of cost-benefit analysis was evaluated by self-reporting on absenteeism and presenteeism from work related to ILI. Costs and benefits of the influenza vaccination from the employer point of view were calculated. Analyses were performed with SPSS 23.0. Results A total of four hundred and twenty-one respondents participated in this study. The influenza vaccination rate in this group was 63.0 % (n=265). The non-vaccinated were 37.0 % (n=156). The rate of ILI was lower among vaccinated (17.0 %) compared to non-vaccinated (47.0 %). The ILI related absenteeism reported was 40.0 % by vaccinated employees compared to 57.5 % by non-vaccinated employee, with absenteeism rate of 0.16 day per employee and 1.05 day per employee respectively. This led to a 6.5 times higher absenteeism rate amongst the non-vaccinated. The influenza vaccination strategy reduced absenteeism due to ILI by 84.8 %. Influenza vaccination was financially beneficial, with savings for employer of up to RM 79.41 per vaccinated employee when only labour cost was included (54.0 % cost saving). The cost saving drastically rise to RM 708.15 (71.0 % cost saving) when the operating income per employee was also incorporated. Conclusions Implementing an influenza vaccination program would reduce the burden o ILI and save substantial amount of financial reserves for the company. This study showed that influenza vaccination for working adults on average is cost saving and cost beneficial when translated into financial investments for the employer. It has significant impact averting cost of absenteeism and presenteeism. The approach on economic evaluation and cost benefit analysis used in this study can be applied to other workplace vaccination strategies in their settings. Keywords: Influenza vaccination, workplace, Influenza Like Illness, absenteeism, presenteeism, cost and benefit.