Objective S. pneumoniae responsible for a range of respiratory infections from uncomplicated to severe invasive pneumococcal disease. Nasopharyngeal specimens were collected from children attending kindergarten and aged ≤ 6 years from February, 2017 to June, 2017 to assess the nasopharyngeal carriage and antimicrobial susceptibility pattern of S. pneumoniae . Parents of children interviewed using questionnaire and check list to identify associated factors. An antimicrobial susceptibility test performed using disk diffusion method. Results Overall pneumococcal carriage were 18.4% (88/477). No significant variation in colonization based on sex and age of children. Children living with siblings (1–2) < 6 years in household (adjusted odd ratio = 16.06; 95% confidence interval 6.21–41.55) and > 5 person per household (adjusted odd ratio = 3.27; 95% confidence interval 1.50–7.14) were associated with higher S. pneumoniae carriage. Non- exclusive breast feeding (adjust odd ratio = 6.00; 95% confidence interval 3.33–10.80) and horse cart transportation (adjusted odd ratio = 2.75; 95% confidence interval 1.05–7.22) increases carriage. S. pneumoniae showed 21 (23.9%) resistance to erythromycin, 18 (20.4%) to amoxicillin, 13 (15.0%) to penicillin, and the least 1 (1.1%) to augmentin.