Time synchronization system using dual frequency bands is designed and the error sources are analyzed for alternative synchronized-pseudolite navigation system (S-PNS) which aims at military application. To resolve near/far problem, dual frequency band operation is proposed instead of pulsing transmission which degrades level of reception. In dual frequency operation H/W delay should be considered to eliminate errors caused by inter-frequency bias (IFB) difference between the receivers of the pseudolites and users. When time synchronization is performed across the sea, multipath error is occurred severely since the elevation angle between pseudolites is low so total reflection can be happened. To investigate the difference of multipath effects according to location, pseudolites are set up coastal area and land area and performances are compared. The error source related with tropospheric delay is becoming dominant source as the coverage of the PNS is broadening. The tropospheric delay is measured by master pseudolite receiver directly using own pseudorange and slave pseudorange. Flight test is performed near coastal area using S-PNS equipped with developed time synchronization system and test results are also presented.