Background Reproductive planning by HIV-infected women is essential, as it helps to prevent transmission of HIV to their unborn babies. Integrating contraceptive services to routine HIV care significantly increases the use of modern contraceptive methods, thus reducing vertical transmission of HIV. Objectives To determine the prevalence and factors associated with contraceptive use among HIV-infected women attending Infectious Disease Clinic (IDC) at Gulu Regional Referral Hospital (GRRH) in Northern Uganda. Methodology A hospital-based cross-sectional study was performed. We used simple random sampling to recruit HIV-infected women receiving routine care from IDC, GRRH, into our study. Sample size was estimated using modified Kish-Leslie formula and semistructured questionnaire was used for data collection. Data was entered into EpiData version 3.1 and analysed using Stata v11.0. We used logistic regression model to assess the associations and any factor with p≤0.05 was considered statistically significant. Results The prevalence of contraceptive use was found to be 36% (95% CI 31 – 40%). Factors which promoted contraceptive use were as follows: being married (aOR=2.68, 95% CI 1.54-4.65, p<0.001) and monthly income of $35 -250 (aOR= 2.38, 95% CI: 1.39- 4.09, p=0.002). Factors that hindered contraceptive use were having no child (nulliparity) (aOR= 0.16; 95% CI: 0.05-0.49; p=0.002) and age range of 31-49 years (aOR= 0.53; 95% CI: 0.33 - 0.84; p=0.007). Conclusion In this study, just over a third of sexually active HIV-infected women reported use of modern contraceptives. This is a low level of usage and, therefore, clinicians and stakeholders should sensitise HIV-infected women on the importance of contraceptive use in the fight against HIV/AIDS and encourage them to use contraceptives to avoid vertical transmission of HIV through unintended pregnancy.