Abstract Much of a child’s early learning takes place during social interactions with others. Neural synchrony, the temporal alignment of individuals’ functional brain activity, is a neural mechanism that may support successful interaction, but its biological origins and sensitivity to environmental factors remain unknown. This study measures neural coherence between 4- to 6-year-old children and their mothers using wearable functional near-infrared spectroscopy (“fNIRS”) in a collaborative problem-solving hyperscanning paradigm. Best practices in fNIRS data processing are incorporated to optimise coherence quantification and extricate environmental- and task-related effects. Results suggest physiological noise in the extracerebral layer artificially inflated coherence strength in both oxygenated (“HbO2”) and deoxygenated (“HbR”) haemoglobin. Coherence remained stronger during collaborative than during individual problem solving in both chromophores after physiological noise reduction. Phase-scrambled pseudodyad analyses supported the interpretation that coherence during collaboration relates to temporal dynamics of interaction rather than to task- or environmental-related components. Strength of HbO2 coherence was positively related to collaborative task performance and negatively related to background maternal stress. HbR coherence was also related to task performance and maternal stress but the direction of results were mixed. Overall, this study provides new insight into the nature of neural coherence between 4- to 6-year-old children and their mothers during collaborative play.