Genome-wide selection (GWS) has been becoming an essential tool in the genetic breeding of long-life species, as it increases the gain per time unit. This study had a hypothesis that GWS is a tool that can decrease the breeding cycle in Jatropha. Our objective was to compare GWS with phenotypic selection in terms of accuracy and efficiency over three harvests. Models were developed throughout the harvests to evaluate their applicability in predicting genetic values in later harvests. For this purpose, 386 individuals of the breeding population obtained from crossings between 42 parents were evaluated. The population was evaluated in random block design, with six replicates over three harvests. The genetic effects of markers were predicted in the population using 811 SNP's markers with call rate = 95% and minor allele frequency (MAF) > 4%. GWS enables gains of 108 to 346% over the phenotypic selection, with a 50% reduction in the selection cycle. This technique has potential for the Jatropha breeding since it allows the accurate obtaining of GEBV and higher efficiency compared to the phenotypic selection by reducing the time necessary to complete the selection cycle. In order to apply GWS in the first harvests, a large number of individuals in the breeding population are needed. In the case of few individuals in the population, it is recommended to perform a larger number of harvests.