In this work, we present BiSSL, a first-of-its-kind training framework that introduces bilevel optimization to enhance the alignment between the pretext pre-training and downstream fine-tuning stages in self-supervised learning. BiSSL formulates the pretext and downstream task objectives as the lower- and upper-level objectives in a bilevel optimization problem and serves as an intermediate training stage within the self-supervised learning pipeline. By more explicitly modeling the interdependence of these training stages, BiSSL facilitates enhanced information sharing between them, ultimately leading to a backbone parameter initialization that is better suited for the downstream task. We propose a training algorithm that alternates between optimizing the two objectives defined in BiSSL. Using a ResNet-18 backbone pre-trained with SimCLR on the STL10 dataset, we demonstrate that our proposed framework consistently achieves improved or competitive classification accuracies across various downstream image classification datasets compared to the conventional self-supervised learning pipeline. Qualitative analyses of the backbone features further suggest that BiSSL enhances the alignment of downstream features in the backbone prior to fine-tuning.