A clean room is used for adjusting the concentration of suspended particles using an air-conditioner. It has a fan-filter unit combining a centrifugal fan and a high-efficiency particulate air filter that purifies the outside air and directly affects its cleanliness. Defects in these systems are typically detected using special sensors for each fault, which can be costly. Therefore, this paper proposes a system for diagnosing defects in the fan-filter unit using a single differential sensor and deep learning. The fan-filter unit is part of the air-conditioning system, and it is usually defective in bearings, filters, and motors. These faults include ball wear, internal bearing contamination, filter contamination, and motor speed changes. Each defect was artificially induced in experiments, and the differential pressure data of each defect was learned using a long short-term memory (LSTM) deep learning algorithm. The results of deep learning experiments generated by randomly mixing data five times were presented using a confusion matrix, and the results showed an accuracy of 87.2±2.60%. Therefore, the possibility of diagnosing defects in the fan-filter unit using a single sensor was confirmed.