Objectives: The aim of the study is to assess the awareness of family medicine residents about influenza and pneumococcal vaccination for high-risk patients and to verify the most significant variables that might affect residents’ knowledge and the tools needed to enhance their practice. Materials and Methods: This cross-sectional study was conducted at four major hospitals in Riyadh, Saudi Arabia, during the period, October through December 2017. A pretested self-administered questionnaire was handed to 180 family residents. Descriptive statistics were used to analyze the study data. The Chi-square test was used to compare categorical variables data. The One-way ANOVA test was used to detect the significant difference. Results: The overall knowledge of physicians about influenza and pneumococcal vaccines was inadequate and was more toward pneumococcal vaccine, in spite their respectable knowledge about the target population. The main reasons for non- prescribing of vaccines were forgetfulness (59.4%), the availability of vaccines (33.9%), and the patients’ refusal (23.3%). The tools that might help for prescribing were the need for the presence of electronic reminder (69.4%) and the patients should follow a regular family physician (47.2%). Conclusion: Knowledge and practice of influenza and pneumococcal vaccination are inadequate. This is mainly because of forgetfulness owing to minimal guideline awareness, lack of vaccine availability, and patients’ refusal. The important recommendations to enhance vaccination practice among physicians are the implementation of electronic reminders, regular follow-up with the same physician in addition to educational programs during residency, and patient education about the importance of vaccinations as a means of disease prevention.