Candida empyema thoracis is a serious complication of invasive candidiasis with high mortality. However, the treatment for Candida empyema remains controversial. We conducted a 9-year retrospective study to analyze the treatments and factors associated with the mortality of patients with Candida empyema thoracis in two medical centers in central Taiwan. The medical records of all patients with positive Candida culture from pleural effusion between October 2002 and September 2011 were reviewed. The demographic data, treatment regimens, and factors associated with mortality were analyzed. During the period of this study, 102 patients were identified. Sixty-three of these patients fulfilled the enrollment criteria, and their data were analyzed. Three-quarters of these patients were male, and the median age of these patients was 69. Thirty-five (55.6%) patients had contiguous infection. The crude mortality rate was 61.9%. Candida albicans was the most common isolate, and malignancy was the most common underlying disease. Patients with advanced age, a higher Charlson's score, shock status, respiratory failure, and noncontiguous infection had a higher mortality rate. Those who had received surgical intervention had a better outcome. In multivariate analysis, the shock status, respiratory failure, and noncontiguous infection source were associated with a higher mortality risk. Candida empyema thoracis is a severe invasive candidiasis with high mortality rate. Shock status, respiratory failure, and noncontiguous infection were factors associated with a higher mortality rate. Surgical intervention or drainage may improve the treatment outcome, especially in patients with contiguous infection.