The use of the faecal immunochemical test (FIT) to stratify the risk of colorectal cancer (CRC) in symptomatic patients in primary healthcare enables improved referrals to colonoscopy. However, its effect on diagnostic delays or the prognosis of patients has been poorly evaluated in this setting. We performed a retrospective cohort study that included symptomatic patients with outpatient CRC diagnosis between 2009 and 2017. We identified whether FIT had been analysed between initial healthcare contact and diagnostic confirmation. We included 589 patients (male = 65%, 71.7 ± 11.6 years, TNM IV = 17.1%) in the analysis. FIT was performed in 411 (69.8%) patients with a positive result (≥10 µg/g of faeces) in 96.4% of the evaluated patients. The use of FIT was associated with increased diagnostic delay (yes = 159 ± 277 days, no = 111 ± 172 days; p = 0.01). At five years follow up, 193 (32.8%) patients died (151 due to CRC). Mean survival was not modified by the use of FIT or its result (not performed = 46.8 ± 1.5 months, FIT+ = 48.9 ± 1 months, FIT− = 45.6 ± 5.5 months; p = 0.5) in Kaplan–Meier analysis, and was confirmed later in multivariate Cox regression analysis. In conclusion, FIT determination in symptomatic patients in primary healthcare did not modify CRC prognosis.