The promising results of clinical trials using immune checkpoint inhibitors revived interests in cancer immunotherapy. However, it also became apparent that efficacy of immune checkpoint blockade can benefit from combining it with immunostimulatory strategies. Here, we review prior and re-emerging approaches using Toll-like Receptor 9 (TLR9) agonists, CpG oligodeoxynucleotides (ODNs), focused on the generation of antitumor immune responses in cancer patients. While numerous early clinical trials using TLR9 ligands in monotherapies provided evidence of CpG ODNs tolerability and safety, they failed to demonstrate sufficient antitumor efficacy. Recent studies unraveled multiple levels of negative regulation of immunostimulatory TLR9 signaling in immune cells by the tumor microenvironment that can stifle immune activity in cancer patients. Therefore, CpG ODNs-based strategies can greatly benefit from combination with strategies targeting immune checkpoint regulation. The most recent clinical trials of CpG ODNs together with immune checkpoint inhibitors have a chance to generate novel, more effective and safer cancer immunotherapies.