The tendon graft is known to undergo a remodeling process after anterior cruciate ligament (ACL) reconstruction. However, little is known about the transcriptional profile of this process. The aim of the present study is to identify differentially expressed genes inside the remodeling ACL graft in the early phase after ACL reconstruction in our murine model using RNA sequencing (RNAseq). Fifty four male C57BL/6 mice were used in this study. The mice were euthanized at 1, 2, and 4 weeks after surgery and used for histological evaluations and RNAseq of the tendon graft. Histologically, there was a progressive decrease in the tendon-bone interface gap space and increased tissue continuity between the grafted tendon and the bone tunnel over time. At 1 and 2 weeks after surgery, cell increase and loss of collagen fiber organization inside the tendon graft were observed. RNAseq showed that genes related to inflammation, matrix metalloproteinases, bone metabolism, chemokines and signaling pathways were upregulated at 1 and 2 weeks after surgery compared to the control group (p < 0.0001). Our transcriptional profiling data suggests that expression of inflammatory mediators and bone remodeling genes may play an important role in the early events in graft-to-bone healing. Further validation at the protein level is necessary to draw firm conclusions about the role of these mediators in graft remodeling and healing. Understanding the remodeling process of the grafted tendons may lead to the identification of new approaches to improve clinical outcomes after ACL reconstruction.