Background: Influenza poses a significant threat to the health of Malaysians, particularly among the elderly population. It results in high levels of illness and mortality, becoming a financial burden on the government. Vaccination is widely recognised as the most effective measure for controlling the spread and impact of influenza. Objectives: This study sought to assess the knowledge, attitudes, and practices (KAP) regarding influenza and influenza vaccination among older adults attending primary healthcare centres in different states of Malaysia. Additionally, the study assessed the level of acceptance for a proposed free annual influenza vaccination program. Methods: A nationwide survey was conducted involving 672 older people aged 60 and above who visited nine primary healthcare centres in Malaysia. These centres were selected using proportionate to population size (PPS) sampling to ensure representation from each zone. Participants completed a validated self-reported questionnaire. Descriptive statistics were used to determine the levels of KAP, and a binomial logistic regression model was used to determine the predictors of acceptance for the proposed free annual vaccination program. Results: Most participants displayed a strong understanding of influenza illness (74.0%) and the vaccine (65.9%). Moreover, 76.4% of respondents exhibited a positive attitude towards influenza vaccination. However, the prevalence of good vaccination practices was relatively low, with only 29.2% of participants having a history of previous vaccination, and just 55.2% of these consistently practicing annual vaccination. The group acceptance rate for the proposed free annual influenza vaccination was 62.3%. Significant predictors of acceptance included a history of previous vaccination (good practice) (OR = 6.438, 95% CI = 1.16–35.71, p < 0.001), a positive attitude towards vaccines (OR = 21.98, 95% CI = 5.44–88.87, p = 0.033), and a good level of knowledge about the influenza vaccine (OR = 0.149, 95% CI = 0.03–0.79, p = 0.026). Conclusions: Increasing the uptake of influenza vaccination among the older population in Malaysia remains a significant challenge. It is recommended that a targeted, free annual influenza vaccination program be implemented for high-risk populations, particularly those with comorbidities and those who have shown greater receptiveness. In addition, health education strategies aimed at raising awareness and understanding of influenza should be prioritised. Strengthening epidemiological data collection and establishing systematic monitoring mechanisms are also essential to support these efforts.