Introduction Discontinuation of a contraceptive method soon after its initiation is becoming a public health problem in Low middle income countries and may result in unintended pregnancy and related unwanted consequences. A better understanding of factors behind discontinuation of a modern method would help in designing interventions to continue its use till desired spacing goals are achieved. Objective To determine factors associated with the discontinuation of modern contraceptive methods within six months of its use compared to continued use of modern method for at least six months in low-income areas of Karachi, Pakistan. Methods A community-based case-control study was conducted in low-income areas of Karachi. Cases were 137 users who discontinued a modern contraceptive method within 6 months of initiation and were not using any method at the time of interview, while controls were 276 continuous users of modern method for at least last six months from the time of interview. Information was collected by using a structured questionnaire. Applied logistic regression was used to identify the associated factors for discontinuation. Results The mean ages of discontinued and continued users were 29.3±5.3 years and 29.2±5.4 years respectively. A larger proportion of the discontinued users had no formal education (43.8%) as compared to the continued users (27.9%). The factors associated with discontinuation of a modern method of contraception were belonging to Sindhi ethnicity [OR: 2.54, 95%CI 1.16-5.57], experiencing side effects [OR: 15.12; 95% CI 7.50-30.51], difficulty in accessing contraceptives by themselves [OR: 0.40, 95%CI 0.19-0.83] and difficulty in reaching clinics for management of the side effects [OR: 4.10, 95%CI 2.38-7.05]. Moreover, women having support from the husband for contraceptive use were less likely to discontinue the method [OR: 0.58, 95% CI 0.34-0.98]. Conclusions Sindhi ethnicity and side effects of modern methods of contraception were identified as major factors for discontinuation in low-income populations. Similarly, women who had difficulty in travelling to reach clinics for treatment also contributed to discontinuation. Furthermore, women using long acting methods and those supported by their husbands were less likely to discontinue the contraceptive methods. Findings emphasize a need to focus on Sindhi ethnicity and trainings of service providers on management of side effects and provision of high quality of services.