Ease of access to health care is of great importance in any country but particularly in countries such as Niger where restricted access can put people at risk of mortality from diseases such as measles, meningitis, polio, pneumonia and malaria. This paper analyzes the physical access of populations to health facilities within Niger with an emphasis on the effect of seasonal conditions and the implications of these conditions in terms of availability of adequate health services, provision of drugs and vaccinations. The majority of the transport within Niger is pedestrian, thus the paper emphasizes access by those walking to facilities for care. Further analysis compared the change in accessibility for vehicular travel since public health workers do travel by vehicle when carrying out vaccination campaigns and related proactive health care activities. Results The majority of the roads in Niger are non-paved (90%). Six districts, mainly in the region of Tahoua lack medical facilities. Patient to health facility ratios were best in Agadez with 7000 people served per health facility. During the dry season 39% of the population was within 1-hours walk to a health center, with the percentage decreasing to 24% during the wet season. Further analyses revealed that vaccination rates were strongly correlated with distance. Children living in clusters within 1-hour of a health center had 1.88 times higher odds of complete vaccination by age 1-year compared to children living in clusters further from a health center (p < 0.05). Three key geographic areas were highlighted where access to health centers took greater than 4 h walk during the wet and dry season. Access for more than 730,000 people can be improved in these areas with the addition of 17 health facilities to the current total of 504 during the dry season (260,000 during the wet season). Conclusions This study highlights critical areas in Niger where health services/facilities are lacking. A second finding is that population served by health facilities will be severely overestimated if assessments are solely conducted during the dry season. Mapped outputs can be used for future decision making processes and analysis.