The United Nations’ Convention on the Rights of Persons with Disabilities mandates people with disabilities to enjoy equal rights in every sphere of their lives including the right to access sexual and reproductive health services (SRHS). However, young people with disabilities (YPWDs) continue to face challenges in accessing these services. This study, therefore, sought to assess the challenges YPWDs face in accessing SRHS in Ghana. The study employed a cross-sectional design and was carried out in 2017 among 2127 in-school YPWDs. Data used for this study were part of a national survey among 16 special schools in Ghana. Data were collected by trained field assistants with pretested questionnaires. The data were entered into the SPSS Version 23 and analysed with the STATA Version 14.2 for Mac OS. The data were analysed using both descriptive (frequencies and percentages) and inferential statistics (binary logistic regression models). The results from the regression analysis were presented as adjusted odds ratios (AORs) with their corresponding 95% confidence intervals (CI) signifying level of precision. Statistical significance was pegged at p value less than 0.05. At the descriptive level, the findings showed that the major challenges YPWDs faced in accessing SRHS are high cost of health services, physical challenges and problem of communication. The logistic regression analysis showed that females (AOR = 0.64, 95% CI = 0.44, 0.92), those in senior high school/technical/commercial (AOR = 0.56, 95% CI = 0.30, 0.75), those in the coastal zone (AOR = 0.47, 95% CI = 0.26, 0.85), the visually impaired (AOR = 0.50, 95% CI = 0.30, 0.82) and those who rated their health status as bad (AOR = 0.45, 95% CI = 0.26, 0.70) had lower odds of facing a challenge in accessing SRHS compared with males, those in primary school, those in the northern zone and those who rated their health status as very good, respectively. Young people with disabilities have challenges accessing SRHS. Therefore, there is the need for the Ministry of Health in collaboration with the Ministry of Education and other stakeholders to make it an intervention priority to train health personnel in the use of sign language and brails to equip them with knowledge and skills to enable them adequately address the challenges YPWDs face in accessing SRHS.