This paper presents a compact, high-performance data acquisition (DAQ) system for silicon photomultiplier (SiPM) array-based positron emission tomography (PET). Several FPGA-embedded DAQ cards have been used for acquiring and processing 18 channels pre-amplified SiPM signals with average pulse width of 320 ns. For each DAQ card, there are 8 channels 105 MHz free-running ADCs, a Xilinx Virtex-4 FPGA and a SDRAM with bandwidth limitation of 450 MB/S. An improved simple digital timing method has been developed which can provide better timing resolution than other digital timing methods. By using an optimized data acquisition method, pulse arrival time, baseline, energy and position for 18 channels input gamma signals can be simultaneously acquired and processed by the on-board FPGA. Coincidence sorting and image reconstruction are based on the analysis of list mode format (LMF) output data. For evaluation on this DAQ system, we measured coincidence timing resolution for two types of recently developed 3 mm x 3 mm SiPM sensors (a fast SiPM and a slow SiPM) using 3 different digital timing methods (initial rise interpolation, digital CFD and maximum rise interpolation). The experimental results show that, initial rise interpolation method provided the best timing resolution for both types of SiPMs: 0.69 ns FWHM for fast SiPM and 1.46 ns FWHM for slow SiPM (digital CFD: 1.49 ns FWHM and 2.22 ns FWHM; maximum rise interpolation: 1.82 ns FWHM and 2.67 ns FWHM). The SDRAM bandwidth limitation problem has been resolved by using the optimized data acquisition method and energy spectra for 8 channels gamma signals from a 3 mm x 3 mm, 4 x 4 SiPM-LYSO array were simultaneous acquired at ADC sampling rate of 100 MHz. Finally, the tomography image for two F-18 line sources was successfully acquired by using a pair of 3 mm x 3 mm, 4 x 4 SiPM-LYSO array detectors. The measured spatial resolution was 3.1 mm FWHM by using OSEM reconstruction method. Based on these experimental results, we conclude that this compact, high-performance DAQ system is reliable and feasible for SiPM array-based PET.