Background Childhood obesity is a serious health condition with increasing rates worldwide. The aim of this study was to investigate the association between inflammation, oxidative stress, vitamin D, copper and zinc in pre-obese and obese children compared to controls. Methods The study involved 202 children aged 7–15 years (63.9% boys), randomly chosen from 10 elementary schools in Podgorica, Montenegro. Participants were divided into three groups according to their nutritional status (International Obesity Task Force [IOTF] criteria): normal-weight (42.1%), pre-obese (40.6%) and obese (17.3%). Serum biochemical analyses were performed (C-reactive protein [CRP], retinol-binding protein [RBP], total antioxidant status [TAS], total vitamin D [VD], copper and zinc). Results Serum TAS and CRP concentrations were higher in pre-obese and obese children compared to controls (p < 0.001). Serum VD concentrations were lower in pre-obese and obese children compared to their normal-weight peers (p = 0.027 and p = 0.054, respectively). Copper, zinc and RBP concentrations did not differ significantly among the groups (p > 0.05). In pre-obese and obese children, a positive correlation was found between CRP and copper (r = 0.305, p = 0.011 and r = 0.440, p = 0.013, respectively), and TAS and RBP (r = 0.528, p < 0.001 and r = 0.434, p = 0.015, respectively). Standard regression analyses showed that CRP and TAS increase (p < 0.001) whereas VD decreases (p = 0.011) with the body mass index (BMI). Conclusions We show that pre-obesity and obesity in childhood are positively associated with oxidative stress and inflammation, and inversely associated with VD status. Copper and zinc concentrations were not associated with excess fat in children.