Fabry disease (FD) is a genetic X-linked, multisystemic, progressive lysosomal storage disorder (LSD). Depression has emerged as a disease complication, with prevalence estimates ranging from 15 to 62%. This is a pilot study examining the effects of psychological counseling for depression in FD on depression, adaptive functioning (AF), quality of life (QOL), and subjective pain experience. Telecounseling was also piloted, as it has beneficial effects in other chronic diseases which make in-person counseling problematic. Subjects completed 6 months of in-person or telecounseling with the same health psychologist, followed by 6 months without counseling. Self-report measures of depression, AF, QOL, and subjective pain were completed every 3 months. All subjects experienced improvements in depression, which were sustained during the follow-up period. Improvements in depression were correlated with improvements in mental health QOL and subjective pain severity, while improvements in mental health QOL were correlated with improvements in AF. While statistical comparison between counseling modes was not possible with the given sample size, relevant observations were noted. Recommendations for future research include replication of results with a larger sample size and a longer counseling period. The use of video counseling may be beneficial. In conclusion, the present pilot study supports the efficacy of psychological treatment for depression in people with FD, highlighting the importance of having health psychologists housed in LSD treatment centers, rather than specialty psychology/psychiatry settings, to increase participation and decrease potential obstacles to access due to perceived stigma.