Information about an individual’s functioning and its longitudinal development is key to informing clinical rehabilitation. However, the description and understanding of the detailed longitudinal course of functioning, i.e., functioning trajectories, is rare in the current SCI literature. The aim of this study was to re-estimate previously identified functioning trajectories of individuals with spinal cord injury (SCI) undergoing initial rehabilitation in Switzerland using trajectory analysis, and to identify highly influential functioning domains that could become trajectory-specific targets for clinical interventions using network analysis. The study was based on data from the Swiss SCI Cohort Study and included individuals with SCI (N = 1099) who completed their rehabilitation in one of four collaborating centers between May 2013 and March 2022. For the trajectory analysis, functioning was operationalized using the total sum score of the Spinal Cord Independence Measure version III (SICM III), which was assessed at up to four time points (T1-T4) during rehabilitation. For the network analysis, individual SCIM III items were used to operationalize relevant functioning problems at T1 (admission) and T4 (discharge). The re-estimation of trajectory analysis confirmed the previously identified mean functioning trajectory classes of stable high functioning (N = 239; 21.75%), early (N = 33; 3.00%), moderate (N = 753; 68.52%), and slow (N = 74; 6.73%) functioning improvement. The network analysis revealed highly connected functioning problems at T1 for the moderate functioning improvement class, including "Feeding", "Dressing upper body", and "Dressing lower body", "Mobility in bed", and "Use of toilet". These functioning domains might indicate potential trajectory-specific targets for clinical interventions. This study has increased our knowledge about functioning trajectories of individuals with SCI undergoing initial rehabilitation in Switzerland and its findings may inform discussions about the application and use of functioning trajectories in clinical practice. Due to the exploratory nature of this study, further research is needed to confirm the findings presented.