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Abstract Networks of weakly coupled oscillators had a profound impact on our understanding of complex systems. Studies on model reconstruction from data have shown prevalent contributions from hypernetworks with triplet and higher interactions among oscillators, in spite that such models were originally defined as oscillator networks with pairwise interactions. Here, we show that hypernetworks can spontaneously emerge even in the presence of pairwise albeit nonlinear coupling given certain triplet frequency resonance conditions. The results are demonstrated in experiments with electrochemical oscillators and in simulations with integrate-and-fire neurons. By developing a comprehensive theory, we uncover the mechanism for emergent hypernetworks by identifying appearing and forbidden frequency resonant conditions. Furthermore, it is shown that microscopic linear (difference) coupling among units results in coupled mean fields, which have sufficient nonlinearity to facilitate hypernetworks. Our findings shed light on the apparent abundance of hypernetworks and provide a constructive way to predict and engineer their emergence.