Objective and accurate classification of fear levels is a socially important task that contributes to developing treatments for Anxiety Disorder, Obsessive–compulsive Disorder, Post-Traumatic Stress Disorder (PTSD), and Phobia. This study examines a deep learning model to automatically estimate human fear levels with high accuracy using multichannel EEG signals and multimodal peripheral physiological signals in the DEAP dataset. The Multi-Input CNN-LSTM classification model combining Convolutional Neural Network (CNN) and Long Sort-Term Memory (LSTM) estimated four fear levels with an accuracy of 98.79% and an F1 score of 99.01% in a 10-fold cross-validation. This study contributes to the following; (1) to present the possibility of recognizing fear emotion with high accuracy using a deep learning model from physiological signals without arbitrary feature extraction or feature selection, (2) to investigate effective deep learning model structures for high-accuracy fear recognition and to propose Multi-Input CNN-LSTM, and (3) to examine the model’s tolerance to individual differences in physiological signals and the possibility of improving accuracy through additional learning.