To examine the associations of apolipoprotein E (APOE) carrier status and lipid profiles with sleep disorders, including excessive daytime sleepiness (EDS) and probable rapid eye movement sleep behavior disorder (pRBD), among patients with early Parkinson's disease (PD) over 5‐year follow‐up periods. The Parkinson's Progression Markers Initiative is a multicenter cohort study based on an ongoing and open‐ended registry. Data from baseline and 5‐year follow‐up visits from participants of de novo PD were analyzed. Longitudinal associations of APOE carrier status and lipid profiles with sleep disorders were estimated via linear mixed‐effects models. A total of 657 participants with complete APOE genotypes were enrolled at baseline. Among them, 153 (25.3%) had available lipid profiles at baseline. In the linear mixed‐effects models, baseline APOE ε2/ε3/ε4 carrier status did not exhibit significant associations with EDS and pRBD (all p > 0.05) in all models. However, reduced high‐density lipoprotein (HDL) and elevated triglycerides (TG) were associated with developing EDS (β = −0.04, 95% CI: −0.07, −0.00) and pRBD (β = 0.01, 95% CI: 0.00, 0.02) in PD patients, respectively. In the APOE ε4+ subgroup, decreased HDL and increased TG displayed substantial associations with developing EDS and sleep disorders (all p < 0.05) in all models, respectively, whereas no significant differences were noted in the APOE ε4− subgroup (all p > 0.05). Our study did not demonstrate a clear association between APOE ε2/ε3/ε4 and sleep disorders in PD patients. However, the presence of APOE ε4 was associated with changes in lipid profiles, notably affecting TG and HDL levels.