BACKGROUND: Advanced HIV disease (AHD) is still a significant problem in Uganda despite the test-and-treat strategy and the increased access to antiretroviral therapy (ART). Meningitis remains a major cause of morbidity and mortality in people with AHD. HIV counselling is essential and plays an important role in managing persons with AHD-related meningitis. We sought to describe the experiences and challenges we faced during counselling of these individuals, highlighting the strategies, gaps and how we can fill them. METHODS: First, we describe our experience and major challenges in counselling people with AHD-related meningitis. Second, we describe the strategies we used to overcome each of these challenges. Third, we highlight the health system gaps and recommend solutions. RESULTS: Major challenges include the presence of altered mental status, unknown HIV status at admission, non-disclosure of HIV status to family, insufficient ART history, caretakers-related challenges, pill burden, multiple drug side effects, invasive clinical procedures, myths about medical procedures, poverty, lack of privacy during counselling in the wards, patients/caretakers seeking alternative non-medical interventions including religious, traditional, and herbal therapies before and after initiating meningitis treatment. CONCLUSIONS: Persons with AHD-related meningitis need daily and special consideration during counselling as part of the package of care to improve treatment outcomes. TRIAL REGISTRATIONS: NCT01075152 (23 Feb 2010), NCT01802385 (28 Feb 2013), ISRCTN42218549 (24 April 2018), ISRCTN72509687 (13 July 2017), NCT04031833 (01 January 2019), ISRCTN15668391 (23 May 2019), ISRCTN18437550 (05/11/2021).