We study the frequency dependence of the frequency shifts of the low-degree p modes measured in the F5V star HD 49933, by analyzing the second run of observations collected by the CoRoT satellite. The 137-day light curve is divided into two subseries corresponding to periods of low and high stellar activity. The activity-frequency relationship is obtained independently from the analysis of the mode frequencies extracted by both a local and a global peak-fitting analyses, and from a cross-correlation technique in the frequency range between 1450 μHz and 2500 μHz. The three methods return consistent results. We show that the frequency shifts measured in HD 49933 present a frequency dependence with a clear increase with frequency, reaching a maximal shift of about 2 μHz around 2100 μHz. Similar variations are obtained between the l = 0 and l = 1 modes. At higher frequencies, the frequency shifts show indications of a downturn followed by an upturn, consistent between the l = 0 and 1 modes. We show that the frequency variation of the p-mode frequency shifts of the solar-like oscillating star HD 49933 has a comparable shape to the one observed in the Sun, which is understood to arise from changes in the outer layers due to its magnetic activity.