Bhutan is one of the few countries in the world to take unprecedented steps to control the spread of COVID-19 in the country. This study aimed to investigate knowledge, attitude, and practice (KAP) and their associated covariates among patients attending Phuentsholing Hospital, Bhutan. Therefore, a cross-sectional study was conducted among patients attending Phuentsholing Hospital in Bhutan between March 17 and April 9, 2021, using an interview-administered questionnaire. The multivariable logistic regression was used to identify statistically significant covariates of good KAP. Further, the association between levels of KAP scores was assessed using Pearson’s correlation coefficient. Of the 441 participants, 54.6% (241) were female. Knowledge, attitude, and practice score were reported by 55.3%, 51.8%, and 83.7% of participants, respectively. Higher education, secondary education, monastic education, and non-formal education were 9 [adjusted odds ratio (AOR) = 9.23; 95% confidence interval (CI) 3.438, 24.797], 3.5 (AOR = 3.5; 95% CI 1.425, 8.619), and 4 (AOR = 3.8; 95% CI 1.199, 12.141) times more likely to report good knowledge than illiterates. A positive attitude was associated with higher (AOR = 2.97; 95% CI 1.154, 7.66) and secondary (AOR = 3.53; 95% CI 1.454, 8.55) education compared to illiteracy. The good practice was associated with higher (AOR = 12.31; 95% CI 2.952, 51.318) and secondary (AOR = 11.5; 95% CI 3.439, 38.476) education compared to illiteracy. Participants in the age groups 26–35 years (AOR = 0.11; 95% CI 0.026, 0.484) and >45 years (AOR = 0.12; 95% CI 0.026, 0.588) were less likely to exhibit good practice compared to those aged 18–25 years. Those working in the private or business sectors were 9 (AOR = 8.81; 95% CI 1.165, 41.455) times more likely to have practice compared to civil servants. There was a weak but positive correlation between knowledge-attitude (r = 0.228), knowledge-practice (r = 0.220), and attitude-practice scores (r = 0.338). The need for health education on COVID-19 to increase knowledge and attitude is highly recommended, and should be focused on the less educated and other vulnerable groups such as farmers and students, as well as those older than 25 years.