Alternative funding programs (AFPs) seek to reduce health plan sponsor costs, for example by excluding specialty drugs from a beneficiary's plan coverage and requiring patients to obtain medications through alternative sources (typically, the manufacturer's patient assistance programs) via an AFP vendor as a third-party. To describe patients' experiences and specialty medication access with AFPs. A survey method consisting of 26 optional single-choice and multiple-choice questions with branching logic divided across 5 sections (related to patient challenges with AFPs) was administered to patients recruited from an experienced AFP online patient panel and a patient advocacy group. The survey assessed patients' awareness of AFPs from their employers, experience with the patient assistance program application process via the AFP vendor, timeliness of medication access (if granted), and/or the health impact of delay in access. All descriptive and exploratory subgroup analyses were conducted by disease area and reported income levels; statistical analyses were carried out for the exploratory analyses. The final sample included 227 patients. Most patients (61% [136/223]) first heard of the AFP as part of their health benefit when trying to obtain their medication. Of 198 patients, 88% reported being stressed because of the medication coverage denial and the uncertainty of obtaining their medication. More than half of patients (54% [115/213]) reported being uncomfortable with the benefits manager from the AFP vendor. On average, patients reported waiting to receive their medication for 68.2 days (approximately 2 months); 24% (51/215) reported the wait for the medication worsened their condition and 64% (138/215) reported the wait led to stress and/or anxiety. Patients who indicated the wait time negatively affected them had considered a job change or left their job at a 3-5-fold higher rate than those who reported no impact from wait time. A significantly higher proportion of patients with hemophilia and other bleeding disorders reported receiving their prescribed medication less often than patients with other conditions (63% [19/30] vs 81% [52/64]; P = 0.022), whereas more patients with lower incomes (<$50,000 vs >$50,000) reported not receiving any medication (12% [7/57] vs 5% [7/129]; P = 0.657), although these differences were not significant. Most patients who obtain their specialty medicines via AFPs reported being uncomfortable with the process and experiencing treatment delays, which may have been linked to disease progression, worsened mental well-being, and consideration of a job change. Employers should be aware of the potential downstream impacts on employee health, retention, and the employee-employer relationship when considering implementing an AFP into their health plan.