Gestational and early postnatal iron deficiency occurs commonly in humans and results in altered behaviors suggestive of striatal dysfunction. We hypothesized that early iron deficiency alters the metabolome of the developing striatum and accounts for abnormalities in striatum-dependent behavior in rats. Sixteen metabolite concentrations from a 9-11 mL volume within the striatum were serially assessed in 10 iron-deficient and 10 iron-sufficient rats on postnatal days 8, 22 (peak anemia), and 37 (following recovery from anemia) using 1H NMR spectroscopy at 9.4 tesla. Chin-elicited bilateral forelimb placing and vibrissae-elicited unilateral forelimb placing were also assessed on these days. Iron deficiency altered metabolites indexing energy metabolism, neurotransmission, glial integrity, and myelination over time (P < 0.05). Successful development of behaviors was delayed in the iron-deficient group (P ≤ 0.01). Alterations in creatine, glucose, glutamine, glutamate, N-acetylaspartate, myoinositol, and glycerophosphorylcholine + phosphorylcholine concentrations accounted for 77-83% of the behavioral variability during peak anemia on postnatal day 22 in the iron-deficient group. Correction of anemia normalized the striatal metabolome but not the behaviors on postnatal day 37. These novel data imply that alterations in the metabolite profile of the striatum likely influence later neural functioning in early iron deficiency.