Potato virus Y (PVY) causes major yield losses in potato (Solanum tuberosum L.) crops worldwide. Over the past few decades, two new PVY strains (PVYN−Wi/N:O and PVYNTN) have become prevalent and widely distributed worldwide. In Kenya, there is limited information on the prevalence and distribution of PVY strains in potato cultivars grown in the farmer’s fields. This is a major limiting factor in making decisions for setting up a basis for PVY control. This study was therefore conducted (a) to determine the present prevalence and distribution of the different PVY strains in cultivars grown in different potato-growing counties and (b) to use this knowledge on virus prevalence and distribution in proposing a strategy for PVY control. To this end, a leaf sampling survey was conducted in 354 potato farms in five major potato-growing counties in Kenya with follow-up surveys in two of the five counties for two more seasons. Collected leaf samples were tested using DAS-ELISA, and those found to be infected with PVY were subjected to reverse transcription polymerase chain reactions (RT-PCR) to determine the PVY strains. Overall PVY prevalence was generally low (8.2%). Out of all the PVY-infected plants, PVYN−Wi/N:O was the most prevalent strain (54.9%) followed by PVYO (28.0%) and PVYNTN (17.1%), while PVYN was not detected. The PVYN−Wi/N:O strain occurred across the three seasons and across the counties but only on specific cultivars. Three cultivars were identified as PVY resistant, and the most widely grown cultivar Shangi (60.2%) had only a low PVY prevalence of 0.6%. This is an indication that this cultivar may have already been useful in minimizing virus prevalence in farmer’s fields. This report is the first prevalence survey of PVY strains and resistance; in addition, the results obtained provide a basis for a major focus on PVY resistance breeding in Kenya.