Introduction Age inappropriate vaccination of children increases the rate of mortality and morbidity. All studies conducted in some areas of Ethiopia were only quantitative in nature and focused on the main cities ignoring rural communities. Objective The objective of this study is to assess vaccination timeliness and associated factors among children in Toke Kutaye district, central Ethiopia. Methods A community-based cross-sectional study with quantitative and qualitative data collection methods was used, for which simple random sampling was used to select 602 mothers/caregivers who have vaccinated children aged 12 to 23 months in the district. The collected data were entered into Epi-data version 3.1 and exported to SPSS version 23 for analysis. Bivariate analysis with a P-value of < 0.25 was used to select candidate variables for multivariate logistic regression. Adjusted odds ratio (AOR) with 95% CI and p-value < 0.05 were used to declare a significant association. Qualitative data responses were classified and then organized by content with thematic analysis. Results A total of 590 respondents responded to the interviews, making a response rate of 98%. In this study, 23.9% (95% CI: 20.4–27.7) of children aged 12–23 months had received all vaccines in the recommended time intervals. Urban residence (AOR: 3.15, 95% CI: 1.56–6.4), participation of pregnant women in conferences (AOR: 2.35, 95% CI: 1.2–4.57), institutional delivery (AOR: 2.5: 95% CI: 1.32–4.20), and sufficient knowledge of mothers (AOR: 3, 95% CI: 1.82–5.10) were significantly associated with the timeliness of childhood vaccination. Qualitative findings revealed that lack of knowledge and lack of information from mothers or caregivers, and inadequate communication with health workers hindered timely vaccination. Conclusion The overall timeliness of the child’s vaccination was low in this study. Residence, participation in a conference, place of delivery, and knowledge of the mothers were predictors of vaccination timeliness. Hence, promoting institutional delivery and increasing pregnant mothers awreness on vaccination timeliness through conference participation is compulsory.