Background: The widespread of chloroquine-resistant Plasmodium falciparum malaria in Kenya lead to the official withdrawal of chloroquine (CQ) drug by the Government as a first-line treatment of uncomplicated P. falciparum malaria in 1999. This study aimed to investigate CQ resistant in Kenya after its withdrawal. Methods: Blood samples were collected on 3M Whatman from patients infected with P. falciparum from Chulaimbo Sub-District Hospital. DNA was extracted using Chelex method for Polymerase chain reaction (PCR) amplification of pfcrt and pfmdr-1 genes. PCR--restrictive fragment length polymorphism was performed using enzymes Apol1 and Afl3 targeting point mutation of K76T and N86Y in pfcrt and pfmdr-1 respectively. The PCR products were sequenced, genotyped and further analyzed for amino acid changes in these codons. Chi square tests were used to test the significance of the findings against previous prevalence results. Results: The frequency of pfcrt wild-type codon K76 (chloroquine sensitive) stood at 76.3% while the mutant type codon 76T (chloroquine resistant) at 23.7%. Likewise, the frequency of the pfmdr-1 wild-type codon N86 was 82.9% (chloroquine sensitive) and mutant codon 86Y (chloroquine resistant) was 17.1%. Conclusion: This study observed that there is a significant (χ2 = 170.1, df=2, p<0.05) increase in CQ sensitivity in 2015 compared to 1999 when it was withdrawn indicating that the prevalence and patterns of point mutations of pfcrt (K76T) and pfmdr-1 (N86Y) is decreasing. This further suggests that CQ-sensitive P. falciparum strains are gradually returning after the withdrawal of CQ from the Kenyan population.