In this paper, we propose an end-to-end (E2E) neural network model to detect autism spectrum disorder (ASD) from children’s voices without explicitly extracting the deterministic features. In order to obtain the decisions for discriminating between the voices of children with ASD and those with typical development (TD), we combined two different feature-extraction models and a bidirectional long short-term memory (BLSTM)-based classifier to obtain the ASD/TD classification in the form of probability. We realized one of the feature extractors as the bottleneck feature from an autoencoder using the extended version of the Geneva minimalistic acoustic parameter set (eGeMAPS) input. The other feature extractor is the context vector from a pretrained wav2vec2.0-based model directly applied to the waveform input. In addition, we optimized the E2E models in two different ways: (1) fine-tuning and (2) joint optimization. To evaluate the performance of the proposed E2E models, we prepared two datasets from video recordings of ASD diagnoses collected between 2016 and 2018 at Seoul National University Bundang Hospital (SNUBH), and between 2019 and 2021 at a Living Lab. According to the experimental results, the proposed wav2vec2.0-based E2E model with joint optimization achieved significant improvements in the accuracy and unweighted average recall, from 64.74% to 71.66% and from 65.04% to 70.81%, respectively, compared with a conventional model using autoencoder-based BLSTM and the deterministic features of the eGeMAPS.