Stability of phase is a critical issue in several applications, especially those that require the transmission of reference signals. A fiber optic system is considered the best medium for the transmission of reference signals due to its high bandwidth, superior stability and immunity to external interference. Even in fiber optic links, phase stability becomes an issue as the microwave frequency of operation is increased. We quantify phase noise in an analog fiber optic system and also study the effect of optical amplification on the noise. The amplifier is placed at three different positions in the link, to check for significant variations in phase noise when no other link parameters are changed. The study also examines how phase noise is affected by changing transmitter power and wavelength. Experimental results indicate fluctuations in phase noise greater than 10dB for different transmitter power outputs while wavelength changes produce very little effect on the noise. Optical amplification increases the average phase noise by 3 to 6dB depending on the location of the amplifier in the link. In addition to experimental studies, computer simulations using Virtual Photonics (VPI) software are performed to confirm experimental results.