Modern contraceptive use has increased globally, but unmet needs persist in low- and middle-income countries. This study in Uganda aimed to examine the prevalence and factors influencing the use of short-acting reversible contraceptives (SARC) like pills and long-term methods such as intrauterine devices. Limited evidence exists on the use of SARC and long-term methods in Uganda. Data from the Africa Medical and Behavioural Sciences Organization (AMBSO) Population Health Surveillance (APHS) in Hoima and Wakiso districts were analysed. Among the 1642 women aged 15–49 years, the prevalence of modern contraceptive use was 30% for SARC, and 18% for long-term method. Women with formal education were three times more likely to use long-term methods than those without formal education, relative risk ratios (RRR), 3.1–3.4, (95%CI 1.2–8.2). Joint decision-making for contraceptive use increased SARC usage, RRR 1.4 (95%CI 1.1–1.8). Urbanization played a role, with women in more urbanized Wakiso district less likely to use any modern contraception, RRR 0.6–0.7 (95%CI 0.5–0.9) compared to those living in the less urbanized Hoima. About half of the women in the study used modern contraceptives and the use of SARC was almost twice that of long-term methods. Increased access to contraception education for all women of reproductive age could significantly improve the use of long-term methods which offer more reliable protection against unintended pregnancies. The findings shed light on the need to strengthen both general and sexuality education to girls and women and to tailor contraception access for all in need, for mobile semi-urban as well as rural women. Well-informed strategies that engage young men and male partners in informed decision-making for contraceptive use could enhance progress.