Pecora interned at New York Hospital-Cornell Medical Center from 1983 to 1984 and was a resident in internal medicine from 1984 to 1986. From 1986 to 1989, he began a fellowship at Memorial Sloan Kettering Cancer Center. He then moved to Hackensack University Medical Center to become assistant director of stem cell and bone marrow transplantation from 1990 to 1993. He went on to become the program's chief director and the director of stem cell collection and storage services. Pecora has later served as the John Theurer Cancer Center's chairman, chief innovations officer, and vice president during his career at the hospital. In 1995, Hackensack was part of a large clinical study sponsored by National Cancer Institute to study the use of bone marrow transplantation to treat women with advanced breast cancer. He expressed his misgivings about only offering the procedure as part of the study as there was a chance the patients would be chosen to be a part of the control group. He instead offered direct access to the popular new procedure as an alternative to participation in the trial, allowing the patients to choose. The procedure was later proven ineffective. In 1998, Pecora started a version of the problem-based learning program at UMDNJ. An adaptation of earlier programs that allows medical students to fulfill their early basic science course requirements by examining the actual case studies. That same year, Pecora was the lead author on the study of CD34+CD33− cells as it relates to chemotherapy treatment and bone marrow transplantation for the treatment of non-Hodgkin's lymphoma. Pecora et al. discovered that patients who had received more than two cycles of chemotherapy and were shown to have "chemotherapy-resistant NHL mobilized a significantly lower percentage of CD34+CD33− cells than did chemotherapy-sensitive NHL patients." They also found the reverse that those who had received less significant levels of chemotherapy treatment had higher levels of CD34+CD33− cells. In 2002, Pecora was an investigator in a study of PV701, a virus that selectively attacks cancer cells. In the Phases 1clinical trial, they found that intravenous administration of the oncolytic viruses led to inflammation of the tumor site that made it difficult to immediately determine effectiveness of the treatment. This false appearance of increase in cancer cells was confirmed by a later trial of the same oncolytic virus and also in Onyx 015, an oncolytic adenovirus. In describing the report authored by Pecora, Emily Bergsland and Alan Venook editorialized that The study concludes that PV701 could be tested relatively safely and offers dosing guidelines to mitigate side effects. However, the study raised more questions, moving "the field forward, even if very slowly." In 2009, The Record named Pecora among Hackensack's administration with conflicts-of-interest, as they had ownership interests in companies with business dealings with the hospital. In 2011, Pecora founded Cota Healthcare, a company to develop a classification system based on patient's "gender, age, family history, type and stage of disease, and treatments."
