Objective To determine the prevalence and possible factors associated with anaemia, and vitamin B 12 and folate deficiencies in women of reproductive age (WRA) in Pakistan. Methods A secondary analysis was conducted on data collected through the large-scale National Nutrition Survey in Pakistan in 2011. Anaemia was defined as haemoglobin levels <12 g/dL, vitamin B 12 deficiency as serum vitamin B 12 levels of <203 pg/mL (150 pmol/L) and folate deficiency as serum folate levels <4 ng/mL (10 nmol/L). Results A total of 11 751 blood samples were collected and analysed. The prevalence of anaemia, vitamin B 12 deficiency and folate deficiency was 50.4%, 52.4% and 50.8%, respectively. After adjustment, the following factors were positively associated with anaemia: living in Sindh province (RR 1.07; 95% CI 1.04 to 1.09) P<0.00, food insecure with moderate hunger (RR 1.03; 95% CI 1.00 to 1.06) P=0.02, four or more pregnancies (RR 1.03; 95% CI 1.01 to 1.05) P<0.00, being underweight (RR 1.03; 95% CI 1.00 to 1.05) P=0.02, being overweight or obese (RR 0.95; 95% CI 0.93 to 0.97) P<0.00 and weekly intake of leafy green vegetables (RR 0.98; 95% CI 0.95 to 1.00) P=0.04. For vitamin B 12 deficiency, a positive association was observed with rural population (RR 0.81; 95% CI 0.66 to 1.00) P=0.04, living in Khyber Pakhtunkhwa province (RR 1.25; 95% CI 1.11 to 1.43) P<0.00 and living in Azad Jammu and Kashmir (RR 1.50; 95% CI 1.08 to 2.08) P=0.01. Folate deficiency was negatively associated with daily and weekly intake of eggs (RR 0.89; 95% CI 0.81 to 0.98) P=0.02 and (RR 0.88; 95% CI 0.78 to 0.99) P=0.03. Conclusions In Pakistan, anaemia, and vitamin B 12 and folate deficiencies are a severe public health concern among WRA. Our findings suggest that further research is needed on culturally appropriate short-term and long-term interventions within communities and health facilities to decrease anaemia, and vitamin B 12 and folate deficiencies among Pakistani women.