Pecan (Carya illinoinensis) is a nut-producing tree native to North America grown for its culinary, ornamental, and lumber characteristics. A newly developed chromosome-scale reference genome for pecan was used to create genotyping-by-sequencing (GBS)-based high-density genetic linkage maps of 151 full-sibling progeny of ‘Elliott’ and ‘VC1-68’. These maps incorporate 6142 SNPs segregating in a testcross pattern into 32 linkage groups representing the 16 chromosomes of pecan across the two parents. The average distance between markers was 0.46 cM and the two maps totaled 1376.4 cM and 1463.1 cM for ‘Elliott’ and ‘VC1-68’, respectively. These markers, plus an additional 1096 intercross markers, were used to create a 1557.8-cM pecan consensus genetic linkage map. Quantitative trait locus (QTL) analyses revealed 1 major and 2 minor effect QTL for budbreak and 1 minor effect QTL for pecan scab susceptibility. The major effect locus inherited from ‘VC1-68’ explained up to 30% of the variation in budbreak and appeared across 3 years of observations. This QTL is syntenic to recently identified major effect QTL for budbreak in English walnut. The techniques reported herein, and the resulting genetic maps will facilitate future discoveries of valuable fruiting trait loci as this pecan population completes the transition to sexual maturity. In addition, the major budbreak QTL coincident in pecan and English walnut may represent a conserved mechanism effecting budbreak across the Juglandaceae providing critical knowledge for future investigations of variability in phenology.