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Little is known about the prevalence of anaemia and associated factors in school children in Vietnam. In this cross-sectional study, we aimed to determine the prevalence of anaemia and its subtypes, and the associations of types of anaemia with demographic, socio-economic and anthropometric factors among 6&#8722;9-year-old primary school children in rural areas of Hai Phong City, Vietnam. Haemoglobin (Hb) and mean corpuscular volume (MCV) were measured, and demographic, socio-economic and anthropometric data were collected in 893 children from eight primary schools. The prevalence of anaemia (Hb &lt; 115 g/L) was 12.9% (95% CI: 8.1%, 19.9%), microcytic anaemia (Hb &lt; 115 g/L and MCV &lt; 80 fL) was 7.9% (95% CI: 5.3%, 11.6%) and normocytic anaemia (Hb &lt; 115 g/L and MCV 80&#8722;90 fL) was 5.3% (95% CI: 2.9%, 9.5%). No child presented with macrocytic anaemia (Hb &lt; 115 g/L and MCV &gt; 90 fL). Children who were underweight, wasted, or in anthropometric failure (either underweight, stunted or wasted) were more likely to be anaemic (all <i>p</i> &#8804; 0.004), and specifically, to have normocytic anaemia (all <i>p</i> &#8804; 0.006), than those who were not underweight, wasted or in anthropometric failure. Stunted children were more likely to be anaemic (<i>p</i> = 0.018) than those who were not stunted. Overweight/obese children were less likely to be anaemic (<i>p</i> = 0.026) or have normocytic anaemia (<i>p</i> = 0.038) compared with children who were not overweight/obese. No anthropometric status indicator was associated with the risk of microcytic anaemia. No demographic or socio-economic factor was associated with any type of anaemia. Anaemia remains a public health issue in rural areas in Hai Phong City, Vietnam, and future approaches for its prevention and control should target undernourished primary school children.