Background: Chronic kidney disease, for which estimated glomerular filtration rate (eGFR) trajectories are early markers, is frequent in people living with HIV. Setting: Identify eGFR trajectory patterns according to kidney function and assess associated factors over a 13-year follow-up period. Methods: We evaluated longitudinal changes and its associated factors in eGFR of 3366 participants according to kidney function with a 2-level, linear, mixed model. Results: Participants with initial kidney dysfunction experienced a slight eGFR increase, whereas others showed a slight decrease. A weak relationship was observed between baseline eGFR and its variation over time. Baseline eGFR was affected by age, CD4 + count, viral load, hypertension, hyperlipidemia, AIDS-defining illness and tenofovir (TDF) with integrase inhibitor (INSTI) or efavirenz. Significant factors for eGFR change included the following: in kidney dysfunction, CD4 + cell count of >350 cells per cubic millimeter and undetectable viral load increased eGFR, whereas TDF + protease inhibitor decreased eGFR; in mildly decreased kidney function, CD4 + cell count of >350 cells per cubic millimeter, AIDS-defining illness, and TDF + efavirenz increased eGFR, whereas age, hypertension, hyperlipidemia, and TDF + INSTI decreased eGFR; in normal kidney function, age, CD4 + cell count of > 350 cells per cubic millimeter, undetectable viral load, hypertension, hyperlipidemia, and TDF + INSTI decreased eGFR, whereas TDF + efavirenz increased eGFR (all P value for interaction < 0.05). Conclusion: Our findings suggest that eGFR trajectories varied widely between individuals in people living with HIV. In the lower eGFR group, virus-related factors were more relevant, whereas traditional risk factors for renal dysfunction were more prominent in the highest eGFR group.