Oocyte in vitro maturation (IVM) and vitrification are being considered as fertility preservation strategies for prepubertal cancer patients. Since prepubertal oocytes have differential sensitivity and response to vitrification compared to adult oocytes, there is a need to optimize the technique to improve the outcome. This study specifically looked into the effect of varying equilibration time and temperatures on the survival and functional competence of prepubertal mouse oocytes. Germinal vesicle (GV) stage and in vitro matured, metaphase II stage sibling oocytes retrieved from 2-week-old Swiss albino mice were equilibrated at 24 °C and 37 °C for 10 and 15 min during vitrification. GV vitrified-IVM (GVV) and GV IVM-vitrified (MIIV) oocytes that survived post-warming were assessed for mitochondrial potential, spindle integrity, spindle checkpoint transcripts, and DNA integrity. The GVV oocytes equilibrated at 37 °C for 15 min had a significantly lower maturation rate (P < 0.01). Survival was reduced when MIIV oocytes were equilibrated at 37 °C, regardless of equilibration duration (P < 0.05). The meiotic spindle and DNA integrity were affected at 37 °C/15 min equilibration (P < 0.01). IVM prepubertal mouse oocytes are at higher risk of experiencing cryo-damage with 37 °C equilibration. Hence, fertility preservation protocols must be refined and individualized for prepubertal age to safeguard the genetic and functional integrity of such oocytes.