The prevalence of tobacco smoking among adolescents aged 13-15 years old in Madagascar was previously reported to be higher than the average in other African regions. A preventive approach is urgently needed to avoid the initiation of early tobacco smoking. Therefore, the aims of this study were to evaluate the status of tobacco smoking among primary schoolchildren in Madagascar and explore the factors associated with initiation of tobacco smoking in the young. This study was conducted in the Mahajanga region of Madagascar. Three primary schools in this region and children of both genders between the ages of nine to 12 years old were randomly selected and approached to participate in this study. A self-administered questionnaire modified from the Global Youth Tobacco Survey Core Questionnaire 2007 was used to assess the status of tobacco smoking among primary schoolchildren. A total of 150 schoolchildren (14.0%) declared that they had smoked tobacco, with 30% starting to smoke tobacco at the age of seven or younger. The prevalence of tobacco smoking was lower among schoolchildren with non-smoking parents (p < 0.001) or non-smoking close friends (p < 0.001). Furthermore, schoolchildren's antismoking intention (p < 0.001) and their knowledge about the harmfulness of tobacco (p = 0.009) had significant effects on the prevalence of tobacco smoking. The results of this study indicate that tobacco smoking among schoolchildren in Madagascar may be influenced by peers, or parents, as well as smoking intention and knowledge about the harmfulness of tobacco use.