This study aimed to assess prescription transfer and medicines collection through Wasfaty, an electronic prescription service recently introduced in Saudi Arabia. A link to a cross-sectional online questionnaire was sent to all students and staff at the University of Jeddah, targeting beneficiaries who received e-prescriptions at the University Medical Centre (n = 2067). The questionnaire comprised 20 items under the following sections; demographics, patient perceptions and satisfaction with the Wasfaty service, and the availability of medicines. Of the 217 questionnaires received, the majority were filled by females (n = 125, 57.6%). Most were satisfied with the initial registration process of Wasfaty (n = 183, 84.1%). However, almost one-third of the participants reported that they could not find the prescribed medicines (n = 64, 29.7%), and most of them had to look for another pharmacy to obtain their treatment (n = 138, 63.9%). Respondents voiced their displeasure owing to the lack of access to certain pharmaceuticals, including anti-hypertensives and antidiabetics. This pilot study identified some challenges relating to the use of the Wasfaty service. Further attention to these challenges is required from the service providers, and a large-scale national study is warranted.