Iron deficiency anaemia remains a public health problem, particularly in children aged 6-59 months. This study assessed factors associated with iron deficiency anaemia among children aged 6-23 months, 24-59 months and 6-59 months in Tanzania. Data for this cross-sectional study were extracted from the 2015-16 Tanzania Demographic and Health Survey and Malaria Indicator Survey (2015-16 TDHS-MIS). The study covered 8014 children aged 6-59 months and their mothers. Iron deficiency anaemia was defined (haemoglobin < 11g/dL). Univariable and multivariable logistic regression analyses that adjust for clustering and sampling weights were conducted to describe the associations between anaemia and potential confounding variables. The prevalence of iron deficiency anaemia among children aged 6-23 months, 24-59 months and 6-59 months were 76%, 49% and 59%, respectively. Factors associated with increased odds of iron deficiency anaemia among children aged 6-23 months included a mother being employed, being a male child, child perceived to small size at birth by mothers, a mother being anaemic and children belonging to the poorest socio-economic quintile. In addition, being a mother with no schooling, children not being dewormed, a mother being anaemic, delivering a baby at home, child fever and stunting, were factors associated with increased odds of iron deficiency anaemia among children aged 24-59 months. Factors associated with increased odds of iron deficiency anaemia among children aged 6-59 months were: a mother being employed, being a mother with no schooling, being a male child, belonging to the 6-59 months age bracket, a mother having a BMI of between 19 and 25 kg/m2, a mother being anaemic, having a baby at home, children belonging to bigger households, child fever and stunting. Interventions to minimise the burden of iron deficiency anaemia in children should target employed and/or anaemic mothers, poor and rich households, as well as male children.