Wheat production losses due to boron (B) toxicity can be reduced by breeding and growing modern wheat cultivars with a greater tolerance to high B. However, breeding of tolerant genotypes is possible by identifying B-tolerant wheat genetic resources and understanding their underlying molecular mechanism. Triticum dicoccum, despite being one of the oldest cultivated wheat species, mostly remained neglected and has been less explored for its potential towards abiotic stresses. In this study, for the first time, we report a B-toxicity-tolerant T. dicoccum genotype, PI94655, and its transcriptomic response towards high-B treatment (10 mM B) using RNA sequencing and RT-qPCR. More than 450 genes were significantly differentially expressed in the shoots of PI94655 under high B. A total 3237 novel genes and 12,206 novel transcripts were determined in the study. AP2-EREBP, MYB, and C3H were the families with the highest percentages of differentially expressed transcription factors (TFs) under B toxicity. Interestingly, KEGG pathway photosynthesis–antenna proteins showed the most significant enrichment. The obtained results suggested potential candidate genes that can be focused on to improve wheat tolerance to high B in future breeding programs. These genes can be functionally characterized to elucidate their role in providing tolerance to high B.