The walnut family Juglandaceae was widely distributed in the Northern Hemisphere while several extant genera now exhibit intercontinental disjunctions. Recent progress in the systematics of Juglandaceae has greatly broadened our knowledge about its origin and evolution. However, there are still uncertainties about the intergeneric relationships within Juglandaceae, and discrepancies between fossil records and inferred divergence times for certain lineages were observed. In this study, well-resolved phylogenies of the Juglandaceae are reconstructed based on both the nuclear RAD-Seq and the whole chloroplast genome data. Our results support the Juglandoideae topology of (Hicoreae, (Platycaryeae, Juglandeae)) at the tribal level. Within Juglandeae, a discordant position of Pterocarya was detected between nuclear and plastid genome data, and a more likely topology (nuclear), ( Juglans, ( Pterocarya, Cyclocarya)), was discussed based on evidence from molecular data and fossil records. Based on carefully selected fossil calibrations, the divergence times of extant lineages were estimated and they corroborated well with fossil records (especially concerning Juglans and Pterocarya). Four sections within Juglans were strongly supported by the nuclear data. Within Juglans, the incongruent position of J. hopeiensis was recovered between the nuclear and plastid genomes. Yet the origin and evolutionary history of J. cinerea and J. hopeiensis are supported to be complicated and need further clarification. Integrative evidence from the fossil records, phylogeny and lineage divergence times shows that Juglandoideae originated in North America, and migrated to Eurasia via both the Bering and the North Atlantic land bridges. Our study shows the potential of integrative biogeographic studies for illuminating the evolutionary history of Juglandaceae.