Background Breast cancer survivors are at higher risk of psychological problems including suicidal ideation. However, studies on suicidal ideation in breast cancer survivors have been rare and have not been investigated prospectively. This study aimed to investigate the prevalence and independent risk factors for suicidal ideation within 1 week and at 1 year after breast surgery for breast cancer. Methods A total of 284 patients with breast cancer were evaluated within 1 week after breast surgery, and 244 (84%) were followed up 1 year later. Suicidal ideation was ascertained using the item ‘suicidal thoughts’ from the Beck Depression Inventory. Various factors potentially related to suicidal ideation were evaluated including sociodemographic and clinical characteristics, and genetic polymorphisms on serotonin and brain‐derived neurotrophic factor (BDNF) systems. Results Suicidal ideation was present in 10.9% of participants at 1 week and 11.4% at 1 year after breast surgery. Suicidal ideation was independently associated with depression and physical disability at 1 week and with living alone, anxiety, advanced cancer stage, and the BDNF met allele (but not with genetic polymorphisms on serotonergic system) at 1 year after breast surgery. Conclusions Suicidal ideation was common and had similar prevalences in both short‐term and longer‐term follow‐ups after breast cancer. However, associated factors were substantially different between the two evaluation points, which suggest that time‐specific programs may be needed for identifying and managing suicidal risk in patients with breast cancer. Copyright © 2013 John Wiley & Sons, Ltd.