The warming of cryopreserved samples supported by small volume devices is governed by heat transfer phenomena which are mathematically described by the solution of the transient heat conduction partial differential equations; the convective heat transfer coefficient (h) is an important parameter involved in the boundary condition which is related to the fluid dynamic behavior at the interface device-warming fluid (water, sucrose solution or air). Unfortunately, h values for small volume devices (i.e. Cryotop®) have not been experimentally determined. Moreover, heat transfer coefficients during warming of Cryotop® cannot be obtained through classical dimensionless correlations expressed in terms of Nusselt vs. Reynolds and Prandtl numbers that are available for regular geometries and single materials. It is the purpose of present work to determine the convective heat transfer coefficients (h) by numerically solving the heat transfer equation applying the finite element method. Numerical simulations allowed to predict time-temperature histories and warming rates under different protocols in Cryotop® system which were compared with literature warming rates reported for this device. The h values were calculated considering the heterogeneous structure of the domain (microdrop, plastic-support) and the irregular three-dimensional geometry. The warming conditions analyzed were: a) open system in contact with air and sucrose solution at 23 °C) and b) closed system in contact with air and water at 23 °C. The h values of the Cryotop® open system immersed in sucrose solution (23 °C), that according to literature achieved a survival in the order of 80%, are in the range of 1800–2200 W/m2K. The h values obtained in this work for warming conditions are critical parameters for cryobiologists when studying heat transfer rate in this small volume device.