In several applications, including in synthetic biology, one often has input/output data on a system composed of many modules, and although the modules' input/output functions and signals may be unknown, knowledge of the composition architecture can significantly reduce the amount of training data required to learn the system's input/output mapping. Learning the modules' input/output functions is also necessary for designing new systems from different composition architectures. Here, we propose a modular learning framework, which incorporates prior knowledge of the system's compositional structure to (a) identify the composing modules' input/output functions from the system's input/output data and (b) achieve this by using a reduced amount of data compared to what would be required without knowledge of the compositional structure. To achieve this, we introduce the notion of modular identifiability, which allows recovery of modules' input/output functions from a subset of the system's input/output data, and provide theoretical guarantees on a class of systems motivated by genetic circuits. We demonstrate the theory on computational studies showing that a neural network (NNET) that accounts for the compositional structure can learn the composing modules' input/output functions and predict the system's output on inputs outside of the training set distribution. By contrast, a neural network that is agnostic of the structure is unable to predict on inputs that fall outside of the training set distribution. By reducing the need for experimental data and allowing module identification, this framework offers the potential to ease the design of synthetic biological circuits and of multi-module systems more generally.