Background The aging of the China population is expected to lead to increasing of nonagenarian and centenarian.The mortality rates of nonagenarian hip fracture patients would return to an equivalent mortality risk to the normal population at five years after injury. It is imperative to evaluate the 5-year mortality for this small but very challenging subgroup patients in order to optimize patient management. The main purpose of the current retrospective study was to compare the five-year survival between arthroplasty treatment and conservative treatment of femoral neck fracture patients age over 90 years during the same 16 -year period.Methods From January 1998 to December 2014, all consecutive nonagenarian and centenarian patients with femoral neck fracture admitted to our hospital were included for evaluation. The primary outcome was defined as thirty-day mortality, 1-year, 3-year, and 5-year mortality after injury. Survival status analysis was performed by the Kaplan–Meier method for mortality. Using the log-rank test, the stratified analyses were performed to compare the difference of overall cumulative mortality and three-time points (1-year, 3-year, and 5-year) mortality after injury were performed to compare the difference of survival distributions.Results Over the 16-year study period, the arthroplasty group and the conservative treatment group included 33 and 53 patients, respectively. The long-term survival probability of the arthroplasty group is significantly higher than the conservative treatment group( p=0.002277). The survival time of the arthroplasty group is significantly higher than the conservative treatment group(Median(P75-P25)=53(59) versus Median(P75-P25)=22(52), p=0.001). The difference of five time points (1-year, 2-year, 3-year, 4-year, and 5-year) mortality between the conservative group and arthroplasty group is significant except for 30-day mortality.The stratified analyses of overall cumulative mortality and three-time points (1-year, 3-year, and 5-year) mortality after injury demonstrated that the arthroplasty group is significant higher than the conservative treatment group.Conclusions Our study demonstrate that, compared with conservative treatment, arthroplasty surgery is more likely to improve the long-term survival of femoral neck fracture patients over 90s. What can be expected is that nearly half of patients will survive more than five years after surgery.