Abstract Objectives The Charlson score is a commonly used measure of comorbidity; however, there is little empirical research into the optimal implementation when studying cancer surgery outcomes using administrative data. We compared four alternative Charlson score implementations, including and excluding metastatic cancer and varying the look-back periods. Study Design and Setting Nine years of linked administrative data were used to identify patients undergoing surgery for cancer of the colon, rectum, or lung in New South Wales, Australia. Four binary outcomes of 30- and 365-day mortality, length of stay greater than 21 days, and emergency readmission within 28 days were compared between groups of similar hospitals. Hospital risk adjustment models were compared for alternative Charlson score implementations. Results Excluding metastatic cancer from the Charlson score improved model performance for short-term outcomes, but there was no implementation that was consistently optimal. Incorporating a look-back period reduced the number of patients for analysis but did not improve hospital risk adjustment. Conclusion Charlson scores for hospital risk adjustment of short-term outcomes of cancer surgery should be calculated excluding metastatic cancer as a separate comorbidity. We found no clear best performing implementation and found no benefit in incorporating any look-back period.