Traditional deep learning (DL) suffers from two core problems. Firstly, it assumes training samples are independent and identically distributed. However, numerous real-world datasets group samples by shared measurements (e.g., study participants or cells), violating this assumption. In these scenarios, DL can show compromised performance, limited generalization, and interpretability issues, coupled with cluster confounding causing Type 1 and 2 errors. Secondly, models are typically trained for overall accuracy, often neglecting underrepresented groups and introducing biases in crucial areas like loan approvals or determining health insurance rates, such biases can significantly impact one's quality of life. To address both of these challenges simultaneously, we present a mixed effects deep learning (MEDL) framework. MEDL separately quantifies cluster-invariant fixed effects (FE) and cluster-specific random effects (RE) through the introduction of: 1) a cluster adversary which encourages the learning of cluster-invariant FE, 2) a Bayesian neural network which quantifies the RE, and a mixing function combining the FE an RE into a mixed-effect prediction. We marry this MEDL with adversarial debiasing, which promotes equality-of-odds fairness across FE, RE, and ME predictions for fairness-sensitive variables. We evaluated our approach using three datasets: two from census/finance focusing on income classification and one from healthcare predicting hospitalization duration, a regression task. Our framework notably enhances fairness across all sensitive variables-increasing fairness up to 82% for age, 43% for race, 86% for sex, and 27% for marital-status. Besides promoting fairness, our method maintains the robust performance and clarity of MEDL. It's versatile, suitable for various dataset types and tasks, making it broadly applicable. Our GitHub repository houses the implementation.