Prevalence of Lyme disease (LD) is increasing in the Netherlands. The Dutch Association for Lyme Disease Patients (NVLP) presented a petition to the Dutch Parliament for more LD research and political attention. The Parliament requested advice from the Health Council of the Netherlands, which among others initiated a stakeholder consultation process to identify experiences and research needs. This article presents patients’ consultation results, including their research agenda, and compares it to the advisory report. Patients ascribed high research priority to improved diagnostic tools, new treatment options, and improving fundamental knowledge. Including patients’ research needs in the advisory report reflected patients’ perspectives in agenda setting to be valued by political and patient institutions. Some issues were not included, leading to criticism by the NVLP. This study suggests that organising a multi-stakeholder dialogue, particularly focusing on further exploring differences in opinion and creating mutual understanding, might have a beneficial effect on stakeholder satisfaction.