Background The objective of this study was to investigate the barriers to follow-up of women with cervical lesions suspicious of cancer who were ineligible for primary-level treatment and needed, but did not receive, hospital-level care in Loreto, Peru. Methods In-depth, semi-structured interviews were conducted with 18 HPV-positive women requiring hospital-level follow-up care for cervical lesions suspicious of cancer but for whom there was no documentation of completion of treatment. After thematically analyzing these patient interviews, interview findings were presented to seven doctors and five nurse-midwives at both the hospital and the primary levels for comments and suggestions regarding barriers to treatment. Finally, all findings were presented at a group model building workshop with 19 health authorities and professionals, where action items were discussed to elicit suggestions for systems-level changes. Results Interviewed patients and healthcare professionals expressed the need to improve communication between levels of care, as well as the need to implement a patient navigation program. Interviewees also discussed the barriers patients encountered in obtaining hospital-level follow-up that ultimately affected their continuum of care. Patient-identified barriers to hospital care were grouped into three main themes: (1) limited patient understanding of treatment steps, (2) the need for multiple trips to the hospital to obtain care, and (3) lack of provider follow-up, leading to their suggestion for (4) the need for patient navigators. The healthcare professionals concurred with the barriers identified by the patients, but further elucidated suggestions for change such as (1) prioritizing patients with a high risk of cancer when referring to the hospital, and (2) increasing communication between the different levels of care. The group model building workshop served as a space to discuss findings and action items that could potentially make these changes possible. Conclusions Despite an overall increase in follow-up for HPV-positive women since the implementation of the new HPV-based screen-and-treat program, women at high risk of developing cervical cancer are still being lost to follow-up after being referred to the hospital for care. The challenges faced by both providers and patients are complex and require systems-level improvements.