Sexual function in female lymphoma survivors after high-dose therapy with autologous stem-cell transplantation (auto-SCT) is largely unstudied. Female lymphoma survivors treated with auto-SCT in Norway 1987-2008 were eligible participants (n = 157). A multi-item questionnaire including a complete Sexual Activity Questionnaire was returned by 70% (n = 110) of the women. A comparison to age-matched normative controls was performed. Sexual inactivity was equal among survivors and controls. The survivors reported personal issues more frequent as reason for inactivity compared with controls (44% vs. 28%, p = 0.04). The sexually active survivors reported more sexual discomfort, greater reduction in frequency of sexual activity, and more sex-related tiredness compared with controls (p value and effect size [95% confidence interval]; p ≤ 0.001, 0.70 [0.44, 0.97], p = 0.03, -0.29 [-0.55, -0.03] and p ≤ 0.001, 0.64 [0.37, 0.90], respectively). Sexual activity was related to older age (odds ratio (OR) 0.58 [0.43, 0.82] per 10 years), being in a relationship (OR 28.6 [6.9, 118.9]) and hormonal replacement therapy (OR 6.0 [1.49, 24.2]). Tiredness in relation to sexual activity was associated with younger age, chronic fatigue and mental distress. Sexual inactivity due to personal issues was more frequent and among those sexually active, a higher rate of sexual dysfunction exists among auto-SCT survivors compared with controls. Hence, sexual function should be addressed at regular timepoints during the cancer trajectory.