Non-Volatile Memory Express (NVMe) over TCP is an efficient technology for accessing remote Solid State Drives (SSDs); however, it may cause a serious interference issue when used in a containerized environment. In this study, we propose a CPU isolation scheme for NVMe over TCP in such an environment. The proposed scheme measures the CPU usage of the NVMe over TCP worker, charges it to containers in proportion to their NVMe traffic, and schedules containers to ensure isolated sharing of the CPU. However, because the worker runs with a higher priority than normal containers, it may not be possible to achieve CPU isolation with container scheduling alone. To solve this problem, we also control the CPU usage of the worker by throttling NVMe over TCP traffic. The proposed scheme is implemented on a real testbed for evaluation. We perform extensive experiments with various workloads and demonstrate that the scheme can provide CPU isolation even in the presence of excessive NVMe traffic.