To expand an areal density of hard disk drives, bit-patterned magnetic recording (BPMR) using a patterned medium instead of a granular medium as employed in perpendicular magnetic recording is attracting much attention as the next-generation recording technology. To further increase the storage capacity of BPMR, multi-layer magnetic recording can be combined with BPMR. Therefore, this paper considers double-layer magnetic recording with a single-reader/two-track reading technique for the staggered BPMR system, which is performed together with a rate-3/5 modulation code. This paper proposes to utilize a multilayer perceptron decoder to decode and estimate the log-likelihood ratio value of the recorded bit sequence that is obtained from the equalized channel. Simulation results show that at a bit-error rate of 10−4, the proposed system with a double-layer recording medium can achieve an improvement gain of about 1.2 decibel if compared to that with a regular single-layer recording medium, even in the presence of media noise.