Background: Effective surveillance and response systems are vital to achievement of disease control and elimination goals. Kenya adopted the revised guidelines of the integrated disease surveillance and response system in 2012. Previous assessments of surveillance system core and support functions in Africa are limited to notifiable diseases with minimal attention given to neglected tropical diseases amenable to preventive chemotherapy (PC-NTDs). The study aimed to assess surveillance system core and support functions relating to PC-NTDs in Kenya. Methods: A mixed method cross-sectional survey was adapted involving 192 health facility workers, 50 community-level health workers and 44 sub-national level health personnel. Data was collected using modified World Health Organization generic questionnaires, observation checklists and interview schedules. Descriptive summaries, tests of associations using Pearson’s Chi-square or Fisher’s exact tests and mixed effects regression models were used to analyse quantitative data. Qualitative data derived from interviews with study participants were coded and analysed thematically. Results: Detection of PC-NTDs was minimal at the peripheral level with limited (60%) use of standard case definitions. Case registration and confirmation capacities were suboptimal at the lower levels with 52% of facilities having functional laboratories. Presence of well-equipped laboratories (p = 0.007), provision for PC-NTDs in reporting forms (p = 0.004) and training of personnel on surveillance (p<0.001) were associated with higher odds of having a functional surveillance system. Lower levels lacked sufficient action thresholds and feedback was limited across all surveillance levels. Supervisory visits frequency at the community (73%) and facility (53%) levels were minimal. Challenges facing PC-NTDs surveillance activities implementation revealed through qualitative data included lack of surveillance guidelines and reporting tools, minimal data analysis, inconsistent feedback, limited supervisory activities, minimal training and low resource provision. Conclusions: Sufficient milestones have been achieved towards improving performance of surveillance functions in Kenya. However, challenges exist relating to PC-NTDs. Core functions including case detection, registration and confirmation, reporting, data analysis and feedback perform sub-optimally at the facility and community levels. Additionally, support functions including standards and guidelines, supervision, training and resources are particularly weak at the sub-national level. Improved PC-NTDs surveillance performance sub-nationally requires strengthened capacities.