Negative symptoms are a key treatment target in early psychosis intervention. There is a paucity of research examining longitudinal course of negative symptoms across the initial years of treatment for first-episode psychosis using individual-based trajectory analysis. No study has been conducted investigating differential relationships of early-stage negative symptom trajectories with long-term distal outcomes. This study examined patterns and baseline predictors of negative symptom trajectories over the first 3 years of treatment in 138 patients aged 18–55 years presenting with first-episode nonaffective psychosis, using latent class growth analysis based on symptom ratings measured at 4 different time points (baseline, 1, 2, and 3 years). We further explored prospective relationships of identified trajectory classes with functional and negative symptom outcomes at 13-year follow-up. Our results revealed 3 distinct negative symptom trajectories including minimal-stable (59.6%), mild-stable (29.4%), and high-increasing (11.0%) trajectories. Poorer premorbid adjustment, more severe global cognitive impairment, and depressive symptoms at baseline were found to predict high-increasing trajectory. Among 3 trajectory classes, patients in high-increasing trajectory had the worst functional and negative symptom outcomes at 13-year follow-up, with post hoc analyses demonstrating significant outcome differences between high-increasing and minimal-stable trajectories. Our findings thus affirm a heterogeneous course of negative symptoms in first-episode psychosis and indicate that early-stage negative symptom trajectories are critically associated with long-term outcomes. Patients displaying persistently high negative symptom levels in the initial 3 years of treatment may represent a specific subgroup who necessitates an extended period of early intervention specifically targeting at negative symptoms to promote early functional recovery.