Detector-based spectral CT offers the possibility of obtaining spectral information from which discrete acquisitions at different energy levels can be derived, yielding so-called virtual monoenergetic images (VMI). In this study, we aimed to develop a jointly optimized deep learning framework based on dual-energy CT pulmonary angiography (DE-CTPA) data to generate synthetic monoenergetic images (SMI) for improving automatic pulmonary embolism (PE) detection in single-energy CTPA scans. For this purpose, we used two data sets: our institutional DE-CTPA data set D1 comprising polyenergetic arterial series and the corresponding VMI at low-energy levels (40 keV) with 7,892 image pairs, and a 10% subset of the 2020 RSNA Pulmonary Embolism Detection Challenge data set D2, which consisted of 161,253 polyenergetic images with dichotomous slice-wise annotations (PE/no PE). We trained a fully convolutional encoder-decoder on D1 to generate SMI from single-energy CTPA scans of D2, which were then fed into a ResNet50 network for training of the downstream PE classification task. The quantitative results on the reconstruction ability of our framework revealed high-quality visual SMI predictions with reconstruction results of 0.984 ± 0.002 (structural similarity) and 41.706 ± 0.547 dB (peak-signal-to-noise ratio). PE classification resulted in an AUC of 0.84 for our model, which achieved improved performance compared to other naive approaches with AUCs up to 0.81. Our study stresses the role of using joint optimization strategies for deep learning algorithms to improve automatic PE detection. The proposed pipeline may prove to be beneficial for computer-aided detection systems and could help rescue CTPA studies with suboptimal opacification of the pulmonary arteries from single-energy CT scanners.