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Understanding others is fundamental to interpersonal coordination and successful cooperation. One mechanism posited to underlie both effective communication and behavioral coordination is interpersonal neural synchrony. Although presumably foundational for children's social development, research on neural synchrony in naturalistic caregiver-child interactions is lacking. Using dual-functional near-infrared spectroscopy (fNIRS), we examined the effects of interaction quality on neural synchrony during a problem-solving task in 42 dyads of mothers and their preschool children. In a cooperation condition, mothers and children were instructed to solve a tangram puzzle together. In an individual condition, mothers and children performed the same task alone with an opaque screen between them. Wavelet transform coherence (WTC) was used to assess the cross-correlation between the two fNIRS time series. Results revealed increased neural synchrony in bilateral prefrontal cortex and temporo-parietal areas during cooperative as compared to individual problem solving. Higher neural synchrony during cooperation correlated with higher behavioral reciprocity and neural synchrony predicted the dyad's problem-solving success beyond reciprocal behavior between mothers and children. State-like factors, such as maternal stress and child agency during the task, played a bigger role for neural synchronization than trait-like factors, such as child temperament. Our results emphasize neural synchrony as a biomarker for mother-child interaction quality. These findings further highlight the role of state-like factors in interpersonal synchronization processes linked to successful coordination with others and in the long-term might improve the understanding of others.