Candidatus Liberibacter asiaticus (CLas) causes the devastating citrus disease Huanglongbing (HLB). Young flushes are the center of the HLB pathosystem due to their roles in the psyllid life cycle and in the acquisition and transmission of CLas. However, the early events of CLas infection and how CLas modulates young flush physiology remain poorly understood. Here, transmission electron microscopy (TEM) analysis showed the mean diameter of the sieve pores decreased in young leaves of HLB-positive trees after CLas infection, consistent with CLas-triggered callose deposition. RNA-Seq-based global expression analysis of young leaves of HLB-positive sweet orange with (CLas-Pos) and without (CLas-Neg) detectable CLas demonstrated a significant impact on gene expression in young leaves, including on the expression of genes involved in host immunity, stress response, and plant hormone biosynthesis and signaling. CLas-Pos and CLas-Neg expression data displayed distinct patterns. The number of upregulated genes was higher than that of the downregulated genes in CLas-Pos for the following categories: plant-pathogen interactions, glutathione metabolism, peroxisome, and calcium signaling that are commonly associated with pathogen infections compared to healthy control. On the contrary, the number of upregulated genes was lower than that of the downregulated genes in CLas-Neg for genes involved in plant-pathogen interactions and peroxisome. Additionally, qRT-PCR based expression analysis temporally visualized the induced expression of companion cell specific genes, phloem protein 2 (PP2) genes, and sucrose transport genes in young flush triggered by CLas. This study advances our understanding of early events during CLas infection of citrus young flushes.