diff --git a/docker/estimate/Dockerfile b/docker/estimate/Dockerfile
deleted file mode 100644
index eb4a7a057..000000000
--- a/docker/estimate/Dockerfile
+++ /dev/null
@@ -1,5 +0,0 @@
-FROM ghcr.io/r-hub/r-minimal/r-minimal:4.4.2
-
-RUN apk upgrade --no-cache
-
-RUN R -e 'install.packages("estimate", repos="http://r-forge.r-project.org", dependencies=TRUE)'
diff --git a/docker/estimate/package.json b/docker/estimate/package.json
deleted file mode 100644
index cd5a502fe..000000000
--- a/docker/estimate/package.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-    "name": "estimate",
-    "version": "2.0.0"
-}
\ No newline at end of file
diff --git a/tools/CHANGELOG.md b/tools/CHANGELOG.md
index a46bab992..c57ce6972 100644
--- a/tools/CHANGELOG.md
+++ b/tools/CHANGELOG.md
@@ -10,6 +10,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
 - Bumped `fastp` memory requirements [#284](https://github.com/stjudecloud/workflows/pull/284)
 
+### Removed
+
+- Removed the long deprecated and unused `estimate.wdl` tool [#292](https://github.com/stjudecloud/workflows/pull/292)
+
 ## 2025 December
 
 ### Changed
diff --git a/tools/estimate.wdl b/tools/estimate.wdl
deleted file mode 100644
index 341eb9b40..000000000
--- a/tools/estimate.wdl
+++ /dev/null
@@ -1,59 +0,0 @@
-## [Homepage](https://bioinformatics.mdanderson.org/estimate/)
-
-version 1.1
-
-task run_estimate {
-    meta {
-        description: "Given a gene expression file, run the ESTIMATE software package"
-        warning: "**[DEPRECATED]**"
-        outputs: {
-            estimate_file: "The results file of the ESTIMATE software package"
-        }
-        deprecated: true
-    }
-
-    parameter_meta {
-        #@ except: DescriptionLength
-        gene_expression_file: "A 2 column headered TSV file with 'Gene name' in the first column and gene expression values (as floats) in the second column. Can be generated with the `calc_tpm` task."
-        outfile_name: "Name of the ESTIMATE output file"
-        memory_gb: "RAM to allocate for task, specified in GB"
-        disk_size_gb: "Disk space to allocate for task, specified in GB"
-        max_retries: "Number of times to retry in case of failure"
-    }
-
-    input {
-        File gene_expression_file
-        String outfile_name = (
-            basename(gene_expression_file, ".TPM.txt") + ".ESTIMATE.gct"
-        )
-        Int memory_gb = 4
-        Int disk_size_gb = 10
-        Int max_retries = 1
-    }
-
-    #@ except: LineWidth, ShellCheck
-    command <<<
-        cp "~{gene_expression_file}" gene_expression.txt
-        Rscript - <<END
-        library("estimate")
-
-        infile <- read.table(file = "gene_expression.txt", sep = '\t', header = TRUE)
-        filtered <- infile[infile$"Gene.name" %in% common_genes[['GeneSymbol']], ]
-        write.table(filtered, sep = "\t", file = "filtered.tsv", row.names = FALSE, quote = FALSE)
-        outputGCT("filtered.tsv", "gene_expression.gct")
-        estimateScore("gene_expression.gct", "common_estimate.gct", platform = "illumina")
-        END
-        mv common_estimate.gct "~{outfile_name}"
-    >>>
-
-    output {
-        File estimate_file = "~{outfile_name}"
-    }
-
-    runtime {
-        memory: "~{memory_gb} GB"
-        disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/estimate:2.0.0"
-        maxRetries: max_retries
-    }
-}
diff --git a/workflows/rnaseq/CHANGELOG.md b/workflows/rnaseq/CHANGELOG.md
index 8bdbc8a96..3031abe92 100644
--- a/workflows/rnaseq/CHANGELOG.md
+++ b/workflows/rnaseq/CHANGELOG.md
@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
  
 The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
+## 2026 January
+
+### Removed
+
+- Removed the long deprecated and unused `ESTIMATE.wdl` tool [#292](https://github.com/stjudecloud/workflows/pull/292)
+
 ## 2025 July
 
 ### Added
diff --git a/workflows/rnaseq/ESTIMATE.wdl b/workflows/rnaseq/ESTIMATE.wdl
deleted file mode 100644
index e8e8a7b01..000000000
--- a/workflows/rnaseq/ESTIMATE.wdl
+++ /dev/null
@@ -1,43 +0,0 @@
-#@ except: DescriptionLength
-
-version 1.1
-
-import "../../tools/estimate.wdl"
-import "../../tools/htseq.wdl"
-
-workflow estimate {
-    meta {
-        name: "ESTIMATE"
-        description: "Runs the ESTIMATE software package on a feature counts file"
-        warning: "**[DEPRECATED]**"
-        external_help: "https://bioinformatics.mdanderson.org/estimate/"
-        outputs: {
-            tpm: "Transcripts Per Million file",
-            estimate_result: "Final output of ESTIMATE",
-        }
-        deprecated: true
-    }
-
-    parameter_meta {
-        counts_file: "A two column headerless TSV file with gene names in the first column and counts (as integers) in the second column. Entries starting with '__' will be discarded. Can be generated with `htseq.wdl`."
-        gene_lengths_file: "A two column headered TSV file with gene names (matching those in the `counts` file) in the first column and feature lengths (as integers) in the second column. Can be generated with `calc-gene-lengths.wdl`."
-    }
-
-    input {
-        File counts_file
-        File gene_lengths_file
-    }
-
-    call htseq.calc_tpm { input:
-        counts = counts_file,
-        feature_lengths = gene_lengths_file,
-    }
-    call estimate.run_estimate { input:
-        gene_expression_file = calc_tpm.tpm_file,
-    }
-
-    output {
-        File tpm = calc_tpm.tpm_file
-        File estimate_result = run_estimate.estimate_file
-    }
-}