We estimated risk factors associated with suspected neuropsychomotor developmental delay at age 2 years, in a birth cohort in the Brazilian Amazon. The Maternal and Child Health and Nutrition in Acre (MINA-Brasil) study is a population-based birth cohort involving children born between July 2015 and June 2016 in the municipality of Cruzeiro do Sul, in the Brazilian state of Acre. We assessed neuropsychomotor development in 735 and 819 children at one and 2 years of age, respectively, using the Denver II screening test. Multivariate Poisson regression models were used to investigate the factors associated with suspected developmental delay at age 2 years. The frequency of suspected developmental delay was 29.5 and 51.0% at one and 2 years of age, respectively, with a cumulative incidence of 41.6% and a persistence of 60.6% between the first and second years of life. After adjustment, the risk of developmental delay at 2 years of age was found to be higher for children born to women with fewer years of education and whose mothers had urinary tract infection during pregnancy. Other risk factors included male sex, low height for age at 2 years, malaria at childhood, pacifier use and limited child stimulation at age 2 years.