The segmented nervous system of bilaterians is organized in structural and functional modules. Modules share across species a robust structural stability. How this robustness is acquired during development is currently unknown. Here, we investigate the sequence of events involved in the establishment of the architectural balance of the nervous system. We demonstrate that a unique robustness pattern is common to the arthropods nervous system plan. This pattern depends on the fine control of the JNK signaling in a subset of early-specified pioneer neurons. JNK activity affects the level of expression of cell adhesion molecules (Fas 2), in part through the modulation of the transcription factor zfh1. A deficit in Fas 2 affects the fasciculation of the axons of primary neurons, leading to secondary bundling defects that result in a general reduction in spatial correlations. Failure to fasciculate affects both architectural robustness and tensional balance, ultimately impeding nervous system condensation.